Starting phenix.real_space_refine on Thu Feb 22 21:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qya_14210/02_2024/7qya_14210_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 S 587 5.16 5 C 64005 2.51 5 N 17410 2.21 5 O 19310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 70": "NH1" <-> "NH2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 247": "NH1" <-> "NH2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a ARG 284": "NH1" <-> "NH2" Residue "a ARG 289": "NH1" <-> "NH2" Residue "b ARG 70": "NH1" <-> "NH2" Residue "c TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "c TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d ARG 175": "NH1" <-> "NH2" Residue "f PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V ARG 368": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "W ASP 407": "OD1" <-> "OD2" Residue "W ARG 408": "NH1" <-> "NH2" Residue "X PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 267": "NH1" <-> "NH2" Residue "Y TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 297": "NH1" <-> "NH2" Residue "Y ARG 312": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 344": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "N TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "Q TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 173": "NH1" <-> "NH2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "T PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 11": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "h TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i ARG 249": "NH1" <-> "NH2" Residue "j ASP 184": "OD1" <-> "OD2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "k PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 66": "NH1" <-> "NH2" Residue "q TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 173": "NH1" <-> "NH2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 182": "NH1" <-> "NH2" Residue "t PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 101325 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1457 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2186 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2115 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "e" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5318 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Chain breaks: 9 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 6286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6286 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 26, 'TRANS': 779} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3807 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 21, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3702 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3008 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3114 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2280 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2892 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2805 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2858 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 362} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2859 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 18, 'TRANS': 356} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2858 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1688 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ILE b 90 " occ=0.41 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.41 residue: pdb=" N SER b 115 " occ=0.85 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.85 residue: pdb=" N ILE b 140 " occ=0.75 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.75 residue: pdb=" N VAL b 173 " occ=0.91 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.91 residue: pdb=" N SER d 70 " occ=0.34 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.34 residue: pdb=" N MET d 144 " occ=0.77 ... (6 atoms not shown) pdb=" CE MET d 144 " occ=0.77 residue: pdb=" N ALA X 359 " occ=0.34 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.34 residue: pdb=" N GLY Z 30 " occ=0.61 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.61 Time building chain proxies: 38.11, per 1000 atoms: 0.38 Number of scatterers: 101325 At special positions: 0 Unit cell: (337.02, 202.76, 205.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 587 16.00 P 12 15.00 O 19310 8.00 N 17410 7.00 C 64005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.02 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.88 Conformation dependent library (CDL) restraints added in 13.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24386 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 490 helices and 80 sheets defined 56.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 47.89 Creating SS restraints... Processing helix chain 'a' and resid 4 through 12 removed outlier: 4.327A pdb=" N LEU a 8 " --> pdb=" O VAL a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 31 removed outlier: 4.041A pdb=" N TRP a 22 " --> pdb=" O GLN a 18 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.651A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 68 removed outlier: 5.259A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 4.441A pdb=" N LEU a 76 " --> pdb=" O ASN a 72 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 104 removed outlier: 4.415A pdb=" N ALA a 93 " --> pdb=" O ASP a 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL a 104 " --> pdb=" O THR a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 126 removed outlier: 4.515A pdb=" N LEU a 123 " --> pdb=" O GLY a 119 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY a 126 " --> pdb=" O LYS a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 143 removed outlier: 3.967A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 166 removed outlier: 6.103A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE a 166 " --> pdb=" O TYR a 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 184 removed outlier: 4.359A pdb=" N LYS a 174 " --> pdb=" O ALA a 170 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 208 removed outlier: 5.277A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU a 208 " --> pdb=" O GLY a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 229 removed outlier: 5.568A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 242 removed outlier: 4.487A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP a 235 " --> pdb=" O GLN a 231 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 257 removed outlier: 4.701A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN a 257 " --> pdb=" O THR a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 282 removed outlier: 4.753A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR a 281 " --> pdb=" O LEU a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 301 Processing helix chain 'a' and resid 304 through 318 removed outlier: 4.748A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 372 Processing helix chain 'b' and resid 24 through 44 removed outlier: 4.206A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 76 removed outlier: 5.445A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.778A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 150 through 162 removed outlier: 3.829A pdb=" N THR b 154 " --> pdb=" O THR b 150 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN b 161 " --> pdb=" O VAL b 157 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 190 removed outlier: 3.926A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'b' and resid 13 through 18 removed outlier: 4.667A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 6.544A pdb=" N LEU c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 4.435A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 4.600A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 169 removed outlier: 4.663A pdb=" N MET c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 164 through 169' Processing helix chain 'c' and resid 178 through 186 removed outlier: 4.038A pdb=" N LYS c 186 " --> pdb=" O GLY c 182 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 197 Processing helix chain 'c' and resid 211 through 228 removed outlier: 4.299A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU c 227 " --> pdb=" O LYS c 223 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 246 through 271 removed outlier: 4.923A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL c 259 " --> pdb=" O TYR c 255 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR c 266 " --> pdb=" O GLU c 262 " (cutoff:3.500A) Proline residue: c 267 - end of helix removed outlier: 6.502A pdb=" N ALA c 271 " --> pdb=" O PRO c 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 273 through 278 removed outlier: 5.077A pdb=" N GLN c 278 " --> pdb=" O ASN c 274 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 307 removed outlier: 6.882A pdb=" N ASP c 289 " --> pdb=" O GLU c 285 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL c 290 " --> pdb=" O GLU c 286 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU c 291 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 33 Processing helix chain 'd' and resid 41 through 66 removed outlier: 6.132A pdb=" N LYS d 45 " --> pdb=" O THR d 41 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU d 48 " --> pdb=" O THR d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 Processing helix chain 'd' and resid 94 through 110 removed outlier: 4.320A pdb=" N LEU d 99 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 4.212A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 124 through 129 removed outlier: 4.828A pdb=" N GLN d 128 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR d 129 " --> pdb=" O LYS d 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 124 through 129' Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.720A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 7.074A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE d 152 " --> pdb=" O TYR d 148 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 162 through 181 removed outlier: 4.672A pdb=" N PHE d 166 " --> pdb=" O SER d 162 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 removed outlier: 3.729A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 3.731A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 257 removed outlier: 4.206A pdb=" N ALA d 243 " --> pdb=" O SER d 239 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU d 248 " --> pdb=" O LYS d 244 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE d 256 " --> pdb=" O GLN d 252 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL d 257 " --> pdb=" O LEU d 253 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.825A pdb=" N ASP e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 55 removed outlier: 3.749A pdb=" N ASP e 51 " --> pdb=" O ASN e 47 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 70 removed outlier: 4.920A pdb=" N TYR e 65 " --> pdb=" O GLU e 61 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET e 67 " --> pdb=" O HIS e 63 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 35 Proline residue: f 28 - end of helix removed outlier: 4.068A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 53 removed outlier: 5.298A pdb=" N LYS f 50 " --> pdb=" O SER f 46 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN f 51 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU f 52 " --> pdb=" O GLU f 48 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN f 53 " --> pdb=" O ASP f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 87 Processing helix chain 'f' and resid 89 through 100 Proline residue: f 93 - end of helix removed outlier: 4.710A pdb=" N LEU f 96 " --> pdb=" O VAL f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 126 Processing helix chain 'f' and resid 128 through 145 Processing helix chain 'f' and resid 163 through 181 removed outlier: 4.126A pdb=" N ALA f 167 " --> pdb=" O ALA f 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 192 removed outlier: 5.332A pdb=" N LEU f 187 " --> pdb=" O PRO f 183 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL f 192 " --> pdb=" O VAL f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 207 through 217 Processing helix chain 'f' and resid 220 through 239 removed outlier: 3.956A pdb=" N ASN f 224 " --> pdb=" O ASP f 220 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS f 228 " --> pdb=" O ASN f 224 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL f 229 " --> pdb=" O ALA f 225 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS f 230 " --> pdb=" O TYR f 226 " (cutoff:3.500A) Processing helix chain 'f' and resid 242 through 260 removed outlier: 3.745A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER f 260 " --> pdb=" O PHE f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 273 removed outlier: 4.525A pdb=" N ALA f 265 " --> pdb=" O ARG f 261 " (cutoff:3.500A) Processing helix chain 'f' and resid 274 through 289 removed outlier: 4.017A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL f 289 " --> pdb=" O CYS f 285 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 309 Processing helix chain 'f' and resid 310 through 325 removed outlier: 4.476A pdb=" N TYR f 314 " --> pdb=" O ASP f 310 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU f 315 " --> pdb=" O VAL f 311 " (cutoff:3.500A) Processing helix chain 'f' and resid 328 through 335 removed outlier: 4.166A pdb=" N ARG f 335 " --> pdb=" O LEU f 331 " (cutoff:3.500A) Processing helix chain 'f' and resid 336 through 350 removed outlier: 6.128A pdb=" N MET f 340 " --> pdb=" O GLU f 336 " (cutoff:3.500A) Proline residue: f 342 - end of helix Proline residue: f 345 - end of helix Processing helix chain 'f' and resid 355 through 360 Processing helix chain 'f' and resid 367 through 382 removed outlier: 6.054A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU f 372 " --> pdb=" O ALA f 368 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN f 382 " --> pdb=" O ASN f 378 " (cutoff:3.500A) Processing helix chain 'f' and resid 389 through 394 removed outlier: 3.924A pdb=" N ASP f 393 " --> pdb=" O LYS f 389 " (cutoff:3.500A) Processing helix chain 'f' and resid 396 through 403 removed outlier: 6.429A pdb=" N TYR f 400 " --> pdb=" O ASN f 396 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS f 401 " --> pdb=" O LYS f 397 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS f 403 " --> pdb=" O LEU f 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 396 through 403' Processing helix chain 'f' and resid 404 through 417 removed outlier: 3.979A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 433 removed outlier: 3.803A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 452 removed outlier: 4.440A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) Processing helix chain 'f' and resid 458 through 466 removed outlier: 4.727A pdb=" N ALA f 462 " --> pdb=" O GLU f 458 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) Processing helix chain 'f' and resid 472 through 489 removed outlier: 3.767A pdb=" N THR f 476 " --> pdb=" O HIS f 472 " (cutoff:3.500A) Processing helix chain 'f' and resid 495 through 505 Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.603A pdb=" N ALA f 515 " --> pdb=" O SER f 511 " (cutoff:3.500A) Processing helix chain 'f' and resid 535 through 549 removed outlier: 4.290A pdb=" N THR f 548 " --> pdb=" O GLU f 544 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) Processing helix chain 'f' and resid 551 through 568 removed outlier: 4.150A pdb=" N ALA f 555 " --> pdb=" O LYS f 551 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 5.286A pdb=" N GLY f 568 " --> pdb=" O LEU f 564 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 582 Processing helix chain 'f' and resid 585 through 601 removed outlier: 4.165A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 619 removed outlier: 3.776A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU f 618 " --> pdb=" O HIS f 614 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS f 619 " --> pdb=" O ILE f 615 " (cutoff:3.500A) Processing helix chain 'f' and resid 620 through 636 removed outlier: 3.609A pdb=" N GLU f 624 " --> pdb=" O PHE f 620 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP f 636 " --> pdb=" O LYS f 632 " (cutoff:3.500A) Processing helix chain 'f' and resid 638 through 643 removed outlier: 4.077A pdb=" N ALA f 642 " --> pdb=" O ASP f 638 " (cutoff:3.500A) Proline residue: f 643 - end of helix No H-bonds generated for 'chain 'f' and resid 638 through 643' Processing helix chain 'f' and resid 645 through 650 removed outlier: 4.957A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) Processing helix chain 'f' and resid 651 through 663 removed outlier: 4.384A pdb=" N LEU f 655 " --> pdb=" O GLY f 651 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY f 663 " --> pdb=" O LEU f 659 " (cutoff:3.500A) Processing helix chain 'f' and resid 668 through 679 removed outlier: 3.914A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 699 Proline residue: f 691 - end of helix removed outlier: 3.855A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL f 699 " --> pdb=" O ALA f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 715 through 728 Proline residue: f 719 - end of helix Processing helix chain 'f' and resid 739 through 754 Processing helix chain 'f' and resid 774 through 786 removed outlier: 3.621A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 5.627A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 790 through 800 removed outlier: 4.008A pdb=" N THR f 798 " --> pdb=" O ALA f 794 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL f 799 " --> pdb=" O GLY f 795 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU f 800 " --> pdb=" O LEU f 796 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 18 removed outlier: 3.727A pdb=" N GLN f 14 " --> pdb=" O VAL f 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN f 15 " --> pdb=" O GLN f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'U' and resid 16 through 31 removed outlier: 4.249A pdb=" N LYS U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 4.659A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.841A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 4.898A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 91 removed outlier: 5.117A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 118 removed outlier: 3.906A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 145 removed outlier: 4.529A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 4.356A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 3.742A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE U 167 " --> pdb=" O PHE U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 188 removed outlier: 3.512A pdb=" N LEU U 181 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS U 182 " --> pdb=" O ALA U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 209 removed outlier: 4.535A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 223 removed outlier: 5.043A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 4.078A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER U 230 " --> pdb=" O PRO U 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 255 removed outlier: 5.398A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE U 248 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N CYS U 249 " --> pdb=" O ALA U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.597A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 329 removed outlier: 3.693A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 346 removed outlier: 5.472A pdb=" N ILE U 335 " --> pdb=" O GLY U 331 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU U 336 " --> pdb=" O GLU U 332 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 5.233A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.997A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 removed outlier: 5.468A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP U 388 " --> pdb=" O GLN U 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 383 through 388' Processing helix chain 'U' and resid 389 through 395 removed outlier: 6.101A pdb=" N LEU U 393 " --> pdb=" O ASN U 389 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA U 394 " --> pdb=" O LEU U 390 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG U 395 " --> pdb=" O GLU U 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 389 through 395' Processing helix chain 'U' and resid 400 through 413 removed outlier: 4.304A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 424 Processing helix chain 'U' and resid 427 through 432 removed outlier: 4.025A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 427 through 432' Processing helix chain 'U' and resid 436 through 451 removed outlier: 4.070A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) Processing helix chain 'U' and resid 458 through 468 removed outlier: 3.564A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 486 removed outlier: 4.220A pdb=" N ARG U 474 " --> pdb=" O ASN U 470 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS U 475 " --> pdb=" O ASP U 471 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY U 477 " --> pdb=" O VAL U 473 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET U 486 " --> pdb=" O GLY U 482 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 502 removed outlier: 4.280A pdb=" N TYR U 494 " --> pdb=" O ARG U 490 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU U 497 " --> pdb=" O VAL U 493 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS U 498 " --> pdb=" O TYR U 494 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 521 removed outlier: 5.432A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 removed outlier: 3.762A pdb=" N GLU U 530 " --> pdb=" O ALA U 526 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR U 535 " --> pdb=" O ASP U 531 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.330A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 574 removed outlier: 4.006A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS U 574 " --> pdb=" O LEU U 570 " (cutoff:3.500A) Processing helix chain 'U' and resid 576 through 591 removed outlier: 4.895A pdb=" N ARG U 580 " --> pdb=" O PRO U 576 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 608 removed outlier: 4.477A pdb=" N ILE U 599 " --> pdb=" O ASN U 595 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG U 600 " --> pdb=" O ASN U 596 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 625 removed outlier: 3.611A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 632 through 642 removed outlier: 4.341A pdb=" N VAL U 636 " --> pdb=" O GLN U 632 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 659 removed outlier: 4.122A pdb=" N LEU U 656 " --> pdb=" O ALA U 652 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY U 657 " --> pdb=" O ALA U 653 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 678 Proline residue: U 674 - end of helix removed outlier: 3.583A pdb=" N ASP U 678 " --> pdb=" O PRO U 674 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.726A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.745A pdb=" N CYS U 703 " --> pdb=" O THR U 699 " (cutoff:3.500A) Proline residue: U 704 - end of helix No H-bonds generated for 'chain 'U' and resid 699 through 704' Processing helix chain 'U' and resid 705 through 720 removed outlier: 4.059A pdb=" N ASP U 719 " --> pdb=" O LYS U 715 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS U 720 " --> pdb=" O VAL U 716 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 removed outlier: 4.227A pdb=" N LYS U 727 " --> pdb=" O ASP U 723 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE U 728 " --> pdb=" O VAL U 724 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 768 removed outlier: 5.084A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) Processing helix chain 'U' and resid 773 through 784 removed outlier: 3.837A pdb=" N HIS U 777 " --> pdb=" O PHE U 773 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 812 removed outlier: 3.865A pdb=" N PHE U 811 " --> pdb=" O LYS U 807 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA U 812 " --> pdb=" O PRO U 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 807 through 812' Processing helix chain 'U' and resid 885 through 890 removed outlier: 5.640A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 removed outlier: 4.070A pdb=" N LEU U 11 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU U 12 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP U 13 " --> pdb=" O SER U 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 8 through 13' Processing helix chain 'V' and resid 26 through 53 Proline residue: V 30 - end of helix removed outlier: 3.820A pdb=" N GLN V 33 " --> pdb=" O PRO V 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA V 42 " --> pdb=" O LYS V 38 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY V 49 " --> pdb=" O GLY V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 76 removed outlier: 4.048A pdb=" N ARG V 65 " --> pdb=" O GLU V 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE V 75 " --> pdb=" O THR V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 97 removed outlier: 4.676A pdb=" N VAL V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU V 95 " --> pdb=" O PRO V 91 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA V 97 " --> pdb=" O PHE V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 119 removed outlier: 3.946A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS V 115 " --> pdb=" O TYR V 111 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL V 117 " --> pdb=" O LEU V 113 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN V 118 " --> pdb=" O TYR V 114 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY V 119 " --> pdb=" O LYS V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 140 Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 147 through 164 removed outlier: 4.058A pdb=" N THR V 151 " --> pdb=" O PHE V 147 " (cutoff:3.500A) Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix removed outlier: 4.740A pdb=" N GLU V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 190 removed outlier: 7.028A pdb=" N ILE V 173 " --> pdb=" O LEU V 169 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 222 removed outlier: 4.425A pdb=" N ALA V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 239 removed outlier: 4.388A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 262 removed outlier: 3.844A pdb=" N TYR V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU V 259 " --> pdb=" O LEU V 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS V 260 " --> pdb=" O ARG V 256 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 273 removed outlier: 6.951A pdb=" N ALA V 267 " --> pdb=" O LEU V 263 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU V 270 " --> pdb=" O GLN V 266 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL V 271 " --> pdb=" O ALA V 267 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER V 272 " --> pdb=" O GLU V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.859A pdb=" N ILE V 298 " --> pdb=" O ARG V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 317 removed outlier: 3.740A pdb=" N ARG V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA V 316 " --> pdb=" O ALA V 312 " (cutoff:3.500A) Proline residue: V 317 - end of helix Processing helix chain 'V' and resid 323 through 339 removed outlier: 5.973A pdb=" N THR V 327 " --> pdb=" O GLY V 323 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL V 335 " --> pdb=" O LEU V 331 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU V 336 " --> pdb=" O LEU V 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 357 Processing helix chain 'V' and resid 360 through 370 removed outlier: 4.834A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 383 removed outlier: 4.675A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY V 383 " --> pdb=" O LEU V 379 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 removed outlier: 3.753A pdb=" N ALA V 388 " --> pdb=" O GLU V 384 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 415 removed outlier: 4.102A pdb=" N ILE V 396 " --> pdb=" O TYR V 392 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 4.717A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN V 427 " --> pdb=" O ALA V 423 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 4.003A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 496 removed outlier: 4.700A pdb=" N HIS V 477 " --> pdb=" O GLN V 473 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE V 496 " --> pdb=" O LYS V 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 9 Processing helix chain 'W' and resid 12 through 18 removed outlier: 4.674A pdb=" N MET W 16 " --> pdb=" O ARG W 12 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL W 18 " --> pdb=" O VAL W 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 12 through 18' Processing helix chain 'W' and resid 21 through 35 removed outlier: 4.564A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 42 through 63 removed outlier: 3.654A pdb=" N LEU W 50 " --> pdb=" O THR W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 87 removed outlier: 4.956A pdb=" N MET W 73 " --> pdb=" O ALA W 69 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 114 removed outlier: 3.760A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA W 100 " --> pdb=" O GLN W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 134 removed outlier: 4.278A pdb=" N ILE W 120 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N MET W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL W 131 " --> pdb=" O THR W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 156 removed outlier: 4.484A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 176 removed outlier: 5.165A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 197 removed outlier: 4.633A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 213 removed outlier: 4.344A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 235 removed outlier: 4.893A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP W 234 " --> pdb=" O MET W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 257 removed outlier: 5.395A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR W 251 " --> pdb=" O TYR W 247 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 4.542A pdb=" N TRP W 263 " --> pdb=" O GLU W 259 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 292 removed outlier: 3.557A pdb=" N SER W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 300 removed outlier: 5.776A pdb=" N GLU W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 293 through 300' Processing helix chain 'W' and resid 301 through 312 removed outlier: 3.502A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR W 311 " --> pdb=" O LYS W 307 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N MET W 312 " --> pdb=" O LEU W 308 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 331 removed outlier: 4.189A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU W 328 " --> pdb=" O TYR W 324 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY W 331 " --> pdb=" O GLU W 327 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 345 through 369 removed outlier: 5.053A pdb=" N LYS W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE W 365 " --> pdb=" O HIS W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 400 removed outlier: 4.340A pdb=" N LEU W 396 " --> pdb=" O PHE W 392 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN W 399 " --> pdb=" O ASN W 395 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 422 through 456 removed outlier: 6.302A pdb=" N ASN W 426 " --> pdb=" O ASN W 422 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP W 427 " --> pdb=" O ASN W 423 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR W 442 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN W 456 " --> pdb=" O ILE W 452 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 60 removed outlier: 3.575A pdb=" N LEU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 81 removed outlier: 3.564A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 3.613A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER X 81 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 101 removed outlier: 4.630A pdb=" N ALA X 86 " --> pdb=" O LYS X 82 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU X 95 " --> pdb=" O SER X 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 3.902A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 141 removed outlier: 3.649A pdb=" N GLN X 127 " --> pdb=" O THR X 123 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU X 129 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 161 removed outlier: 5.559A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN X 152 " --> pdb=" O HIS X 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 3.578A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL X 169 " --> pdb=" O LEU X 165 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU X 172 " --> pdb=" O GLU X 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS X 178 " --> pdb=" O SER X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 removed outlier: 4.056A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 205 through 222 removed outlier: 5.383A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU X 222 " --> pdb=" O HIS X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.193A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 262 removed outlier: 4.177A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS X 252 " --> pdb=" O ILE X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 Processing helix chain 'X' and resid 274 through 280 Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.950A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.941A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 317 removed outlier: 4.292A pdb=" N ASP X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP X 316 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Proline residue: X 317 - end of helix No H-bonds generated for 'chain 'X' and resid 311 through 317' Processing helix chain 'X' and resid 318 through 344 removed outlier: 4.702A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Proline residue: X 341 - end of helix Processing helix chain 'X' and resid 362 through 371 removed outlier: 6.121A pdb=" N SER X 366 " --> pdb=" O GLU X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 421 removed outlier: 3.637A pdb=" N TYR X 397 " --> pdb=" O VAL X 393 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN X 405 " --> pdb=" O LEU X 401 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER X 408 " --> pdb=" O ILE X 404 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 421 " --> pdb=" O LYS X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 30 Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 32 through 47 removed outlier: 4.942A pdb=" N ALA Y 36 " --> pdb=" O ARG Y 32 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 60 removed outlier: 4.041A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 95 removed outlier: 5.160A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN Y 94 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 removed outlier: 4.076A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 131 removed outlier: 4.559A pdb=" N LEU Y 121 " --> pdb=" O LYS Y 117 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG Y 125 " --> pdb=" O LEU Y 121 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS Y 126 " --> pdb=" O THR Y 122 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 4.339A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET Y 152 " --> pdb=" O GLY Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 removed outlier: 5.470A pdb=" N ILE Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR Y 158 " --> pdb=" O ASN Y 154 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER Y 166 " --> pdb=" O GLU Y 162 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU Y 167 " --> pdb=" O LYS Y 163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU Y 169 " --> pdb=" O LYS Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 192 removed outlier: 4.123A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG Y 192 " --> pdb=" O CYS Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 208 removed outlier: 4.784A pdb=" N ALA Y 197 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR Y 204 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL Y 205 " --> pdb=" O PHE Y 201 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR Y 207 " --> pdb=" O ASP Y 203 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE Y 208 " --> pdb=" O THR Y 204 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 228 Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 244 through 254 removed outlier: 4.307A pdb=" N GLU Y 248 " --> pdb=" O ALA Y 244 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU Y 253 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.559A pdb=" N CYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 283 removed outlier: 5.181A pdb=" N PHE Y 271 " --> pdb=" O ARG Y 267 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS Y 283 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 312 Proline residue: Y 290 - end of helix removed outlier: 6.823A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR Y 295 " --> pdb=" O HIS Y 291 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU Y 309 " --> pdb=" O SER Y 305 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR Y 311 " --> pdb=" O LEU Y 307 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG Y 312 " --> pdb=" O LEU Y 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 324 removed outlier: 4.146A pdb=" N ALA Y 322 " --> pdb=" O TYR Y 318 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY Y 324 " --> pdb=" O ALA Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 340 removed outlier: 4.754A pdb=" N ASP Y 331 " --> pdb=" O VAL Y 327 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN Y 332 " --> pdb=" O GLU Y 328 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU Y 333 " --> pdb=" O PHE Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 362 through 387 removed outlier: 4.278A pdb=" N TYR Y 366 " --> pdb=" O LYS Y 362 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN Y 367 " --> pdb=" O ASN Y 363 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU Y 368 " --> pdb=" O TRP Y 364 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE Y 370 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU Y 377 " --> pdb=" O GLY Y 373 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE Y 387 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 3.887A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS Z 22 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY Z 30 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 87 Processing helix chain 'Z' and resid 102 through 117 removed outlier: 4.796A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 167 through 177 removed outlier: 6.132A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL Z 172 " --> pdb=" O GLU Z 168 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS Z 174 " --> pdb=" O VAL Z 170 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG Z 177 " --> pdb=" O GLU Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 217 removed outlier: 4.399A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 236 removed outlier: 4.705A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 287 removed outlier: 3.794A pdb=" N PHE Z 249 " --> pdb=" O PHE Z 245 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN Z 277 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 72 removed outlier: 3.678A pdb=" N LYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.299A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.942A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.090A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.642A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.856A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 4.478A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 247' Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.013A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.516A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 281' Processing helix chain 'A' and resid 292 through 307 removed outlier: 4.321A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 348 through 363 removed outlier: 4.385A pdb=" N THR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 5.643A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 4.414A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 4.118A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 6.780A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 426' Processing helix chain 'B' and resid 66 through 84 removed outlier: 4.723A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.583A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.223A pdb=" N LEU B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 190 through 206 removed outlier: 6.079A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.805A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.814A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.894A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.838A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 318 removed outlier: 5.059A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.773A pdb=" N LYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.938A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 431 removed outlier: 3.878A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.101A pdb=" N LEU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 256 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 68 removed outlier: 4.507A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 147 through 152 removed outlier: 4.818A pdb=" N ILE C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 152' Processing helix chain 'C' and resid 154 through 171 removed outlier: 5.442A pdb=" N ILE C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 3.652A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 removed outlier: 4.278A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.559A pdb=" N PHE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C 241 " --> pdb=" O MET C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.962A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.985A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.558A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 82 removed outlier: 4.029A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 48 " --> pdb=" O TYR D 44 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.206A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 125' Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.476A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 removed outlier: 3.966A pdb=" N ILE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 removed outlier: 4.018A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.428A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 4.759A pdb=" N ILE D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 299 removed outlier: 6.442A pdb=" N ARG D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.733A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 337 through 353 removed outlier: 3.629A pdb=" N SER D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 4.630A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.054A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.845A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.724A pdb=" N ILE D 167 " --> pdb=" O TYR D 164 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLY D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 237 removed outlier: 4.548A pdb=" N PHE D 235 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 236 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN D 237 " --> pdb=" O GLU D 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 51 removed outlier: 4.832A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.098A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.156A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 4.469A pdb=" N ILE E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 136' Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.236A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.801A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 removed outlier: 3.931A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.551A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.571A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.913A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.629A pdb=" N ARG E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.515A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 4.760A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 3.829A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 382 removed outlier: 3.854A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 5.437A pdb=" N ILE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASP E 205 " --> pdb=" O SER E 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 205' Processing helix chain 'F' and resid 45 through 83 removed outlier: 3.853A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.539A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.881A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.820A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.465A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.906A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.395A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 258' Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.718A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.276A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 317 removed outlier: 4.709A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.064A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 removed outlier: 6.041A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET F 373 " --> pdb=" O HIS F 369 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.558A pdb=" N LEU F 384 " --> pdb=" O ASN F 380 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.736A pdb=" N ARG F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.593A pdb=" N TYR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 5.063A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 5.322A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 83 through 105 Processing helix chain 'G' and resid 110 through 129 removed outlier: 5.100A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.803A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 5.375A pdb=" N THR G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 58 through 63 removed outlier: 4.994A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 63' Processing helix chain 'H' and resid 80 through 102 removed outlier: 3.687A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 3.676A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 3.865A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 233 removed outlier: 3.503A pdb=" N ALA H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 removed outlier: 4.394A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 6.662A pdb=" N LEU I 110 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 179 removed outlier: 5.268A pdb=" N ALA I 170 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 212 removed outlier: 3.697A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 250 removed outlier: 4.024A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.782A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 5.002A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 55 through 60' Processing helix chain 'J' and resid 77 through 98 Processing helix chain 'J' and resid 103 through 122 removed outlier: 5.570A pdb=" N ASN J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 179 through 184 removed outlier: 4.517A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP J 184 " --> pdb=" O ALA J 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 179 through 184' Processing helix chain 'J' and resid 185 through 198 Processing helix chain 'J' and resid 221 through 240 removed outlier: 4.345A pdb=" N GLU J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.782A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 5.003A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG j 60 " --> pdb=" O GLU j 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 55 through 60' Processing helix chain 'j' and resid 77 through 98 Processing helix chain 'j' and resid 103 through 122 removed outlier: 5.571A pdb=" N ASN j 122 " --> pdb=" O TYR j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 Processing helix chain 'j' and resid 179 through 184 removed outlier: 4.867A pdb=" N ASP j 184 " --> pdb=" O ALA j 180 " (cutoff:3.500A) Processing helix chain 'j' and resid 185 through 198 Processing helix chain 'j' and resid 221 through 240 removed outlier: 4.345A pdb=" N GLU j 226 " --> pdb=" O PRO j 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 removed outlier: 4.204A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 Processing helix chain 'K' and resid 108 through 123 removed outlier: 4.274A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 211 through 216 removed outlier: 4.329A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU K 216 " --> pdb=" O ALA K 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 211 through 216' Processing helix chain 'K' and resid 231 through 241 removed outlier: 6.265A pdb=" N GLU K 235 " --> pdb=" O LYS K 231 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.671A pdb=" N TYR k 26 " --> pdb=" O PHE k 22 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 Processing helix chain 'k' and resid 108 through 123 removed outlier: 4.273A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN k 122 " --> pdb=" O ASN k 118 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE k 123 " --> pdb=" O LEU k 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.329A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU k 216 " --> pdb=" O ALA k 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 211 through 216' Processing helix chain 'k' and resid 231 through 241 removed outlier: 6.265A pdb=" N GLU k 235 " --> pdb=" O LYS k 231 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU k 236 " --> pdb=" O GLU k 232 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 4.000A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 removed outlier: 4.096A pdb=" N ALA L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 122 removed outlier: 3.686A pdb=" N LEU L 108 " --> pdb=" O PRO L 104 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 164 through 176 removed outlier: 4.613A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 182 removed outlier: 4.433A pdb=" N GLU L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 5.303A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 235 removed outlier: 5.561A pdb=" N VAL L 229 " --> pdb=" O ASP L 225 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 5.693A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 4.000A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 4.096A pdb=" N ALA l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER l 95 " --> pdb=" O GLU l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 122 removed outlier: 3.685A pdb=" N LEU l 108 " --> pdb=" O PRO l 104 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 164 through 176 removed outlier: 4.612A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) Processing helix chain 'l' and resid 177 through 182 removed outlier: 4.432A pdb=" N GLU l 181 " --> pdb=" O SER l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 5.303A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 235 removed outlier: 5.562A pdb=" N VAL l 229 " --> pdb=" O ASP l 225 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 5.693A pdb=" N GLY l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 34 removed outlier: 3.960A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 4.220A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 180 removed outlier: 5.075A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 202 removed outlier: 3.960A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL M 200 " --> pdb=" O ILE M 196 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 233 removed outlier: 4.777A pdb=" N ARG M 232 " --> pdb=" O PRO M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.530A pdb=" N TYR M 238 " --> pdb=" O GLU M 234 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU M 241 " --> pdb=" O LYS M 237 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 34 removed outlier: 3.960A pdb=" N VAL m 30 " --> pdb=" O ALA m 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU m 31 " --> pdb=" O MET m 27 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER m 34 " --> pdb=" O VAL m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 125 removed outlier: 4.219A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 180 removed outlier: 5.076A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLN m 180 " --> pdb=" O ILE m 176 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 202 removed outlier: 3.960A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL m 200 " --> pdb=" O ILE m 196 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP m 202 " --> pdb=" O TYR m 198 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 233 removed outlier: 4.777A pdb=" N ARG m 232 " --> pdb=" O PRO m 228 " (cutoff:3.500A) Processing helix chain 'm' and resid 234 through 243 removed outlier: 3.528A pdb=" N TYR m 238 " --> pdb=" O GLU m 234 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU m 241 " --> pdb=" O LYS m 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 removed outlier: 3.867A pdb=" N THR N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 91 Processing helix chain 'N' and resid 131 through 142 removed outlier: 4.151A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA N 141 " --> pdb=" O GLY N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'n' and resid 48 through 71 removed outlier: 3.867A pdb=" N THR n 52 " --> pdb=" O SER n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 91 Processing helix chain 'n' and resid 131 through 142 removed outlier: 4.150A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP n 140 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA n 141 " --> pdb=" O GLY n 137 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.702A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.577A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 4.365A pdb=" N ASP O 166 " --> pdb=" O GLY O 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.701A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.577A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 removed outlier: 4.366A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 8 removed outlier: 5.189A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 3 through 8' Processing helix chain 'P' and resid 56 through 79 removed outlier: 4.052A pdb=" N GLY P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 3.661A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 5.178A pdb=" N MET P 146 " --> pdb=" O CYS P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.683A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 8 removed outlier: 5.188A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 3 through 8' Processing helix chain 'p' and resid 56 through 79 removed outlier: 4.051A pdb=" N GLY p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 3.660A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 5.179A pdb=" N MET p 146 " --> pdb=" O CYS p 142 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.683A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 71 removed outlier: 3.524A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 4.137A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.248A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 171 removed outlier: 3.811A pdb=" N ARG Q 170 " --> pdb=" O GLU Q 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 71 removed outlier: 3.524A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 4.137A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.249A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 171 removed outlier: 3.810A pdb=" N ARG q 170 " --> pdb=" O GLU q 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE q 171 " --> pdb=" O LEU q 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 71 removed outlier: 3.642A pdb=" N CYS R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.945A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.538A pdb=" N ALA R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 199 Processing helix chain 'r' and resid 48 through 71 removed outlier: 3.642A pdb=" N CYS r 52 " --> pdb=" O GLY r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 75 through 91 removed outlier: 3.945A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.538A pdb=" N ALA r 135 " --> pdb=" O GLY r 131 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 199 Processing helix chain 'S' and resid 57 through 79 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.753A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.955A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 79 Processing helix chain 's' and resid 84 through 100 removed outlier: 3.754A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.956A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.695A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.983A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.461A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.711A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.695A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.983A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.461A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.712A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'g' and resid 22 through 35 removed outlier: 4.451A pdb=" N GLU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 5.322A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 Processing helix chain 'g' and resid 110 through 129 removed outlier: 5.099A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 185 removed outlier: 3.803A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 5.375A pdb=" N THR g 194 " --> pdb=" O THR g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 243 Processing helix chain 'h' and resid 19 through 32 Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.995A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 80 through 102 removed outlier: 3.687A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 125 removed outlier: 3.962A pdb=" N GLY h 125 " --> pdb=" O TYR h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.677A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 3.865A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU h 209 " --> pdb=" O GLU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 209' Processing helix chain 'h' and resid 222 through 233 removed outlier: 3.502A pdb=" N ALA h 231 " --> pdb=" O LYS h 227 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA h 232 " --> pdb=" O ASP h 228 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE h 233 " --> pdb=" O TYR h 229 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 31 removed outlier: 4.393A pdb=" N GLU i 22 " --> pdb=" O LEU i 18 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 Processing helix chain 'i' and resid 106 through 124 removed outlier: 6.662A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 179 removed outlier: 5.269A pdb=" N ALA i 170 " --> pdb=" O ASN i 166 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 201 Processing helix chain 'i' and resid 207 through 212 removed outlier: 3.697A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 250 removed outlier: 4.025A pdb=" N VAL i 233 " --> pdb=" O LYS i 229 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'a' and resid 321 through 326 removed outlier: 5.862A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER a 323 " --> pdb=" O HIS a 332 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS a 332 " --> pdb=" O SER a 323 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP a 325 " --> pdb=" O ARG a 330 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 47 through 53 removed outlier: 4.240A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR b 6 " --> pdb=" O ASN b 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY b 50 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET b 7 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE b 110 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS b 9 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA b 111 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL b 113 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY b 167 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS b 169 " --> pdb=" O VAL b 138 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 52 through 58 removed outlier: 4.349A pdb=" N VAL c 53 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA c 142 " --> pdb=" O PHE c 160 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE c 160 " --> pdb=" O ALA c 142 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 65 through 69 removed outlier: 4.818A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'U' and resid 786 through 789 removed outlier: 5.872A pdb=" N THR U 786 " --> pdb=" O VAL U 884 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL U 884 " --> pdb=" O THR U 786 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'U' and resid 802 through 805 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'U' and resid 899 through 902 removed outlier: 6.332A pdb=" N ARG U 899 " --> pdb=" O THR U 917 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Z' and resid 8 through 11 Processing sheet with id= 9, first strand: chain 'Z' and resid 120 through 124 removed outlier: 3.746A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 120 through 124 removed outlier: 7.003A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 140 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 101 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 138 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.532A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 318 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 210 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 317 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 107 through 112 removed outlier: 4.935A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 121 through 125 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'B' and resid 245 through 250 removed outlier: 3.924A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 225 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 94 through 98 removed outlier: 7.382A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 114 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 115 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR C 122 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 209 through 213 removed outlier: 3.901A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET C 293 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 109 through 114 removed outlier: 4.318A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL D 88 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 226 through 230 removed outlier: 5.484A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG D 200 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 307 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 203 " --> pdb=" O ARG D 329 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 61 through 64 removed outlier: 6.301A pdb=" N LYS E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 97 through 100 removed outlier: 4.291A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'E' and resid 194 through 199 removed outlier: 4.250A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS E 228 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 279 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 95 through 98 removed outlier: 4.001A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 159 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.528A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.956A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.604A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.128A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.565A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 134 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.690A pdb=" N VAL H 44 " --> pdb=" O CYS H 213 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.018A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE I 37 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU I 44 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.432A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 76 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER I 75 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'J' and resid 69 through 74 removed outlier: 3.791A pdb=" N SER J 130 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.656A pdb=" N ALA J 32 " --> pdb=" O ILE J 161 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'j' and resid 69 through 74 removed outlier: 3.792A pdb=" N SER j 130 " --> pdb=" O ALA j 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'j' and resid 158 through 162 removed outlier: 3.657A pdb=" N ALA j 32 " --> pdb=" O ILE j 161 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU j 208 " --> pdb=" O LEU j 220 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'K' and resid 67 through 70 removed outlier: 4.092A pdb=" N VAL K 68 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY K 144 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.109A pdb=" N ALA K 37 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'k' and resid 67 through 70 removed outlier: 4.093A pdb=" N VAL k 68 " --> pdb=" O CYS k 76 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY k 144 " --> pdb=" O GLY k 75 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU k 153 " --> pdb=" O CYS k 165 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'k' and resid 167 through 171 removed outlier: 4.110A pdb=" N ALA k 37 " --> pdb=" O ILE k 170 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'L' and resid 71 through 75 removed outlier: 3.603A pdb=" N LEU L 133 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 75 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'L' and resid 158 through 162 removed outlier: 5.037A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER L 211 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'l' and resid 71 through 75 removed outlier: 3.603A pdb=" N LEU l 133 " --> pdb=" O SER l 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA l 75 " --> pdb=" O GLY l 131 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.036A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER l 211 " --> pdb=" O ALA l 48 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.385A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY M 74 " --> pdb=" O GLY M 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA M 76 " --> pdb=" O MET M 136 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET M 136 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.120A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 66 through 69 removed outlier: 6.385A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY m 74 " --> pdb=" O GLY m 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA m 76 " --> pdb=" O MET m 136 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET m 136 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.119A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.475A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER N 46 " --> pdb=" O GLY N 97 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.218A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.475A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER n 46 " --> pdb=" O GLY n 97 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.217A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.367A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL O 103 " --> pdb=" O ASN O 40 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU O 110 " --> pdb=" O LEU O 122 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR O 114 " --> pdb=" O SER O 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 124 through 128 removed outlier: 5.106A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP O 17 " --> pdb=" O THR O 2 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.366A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL o 103 " --> pdb=" O ASN o 40 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU o 110 " --> pdb=" O LEU o 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR o 114 " --> pdb=" O SER o 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER o 118 " --> pdb=" O TYR o 114 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 124 through 128 removed outlier: 5.105A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP o 17 " --> pdb=" O THR o 2 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'P' and resid 42 through 45 removed outlier: 4.520A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.656A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.519A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.655A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Q' and resid 41 through 48 removed outlier: 5.789A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 129 through 132 removed outlier: 4.749A pdb=" N ALA Q 130 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS Q 132 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Q 13 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR Q 177 " --> pdb=" O ARG Q 19 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE Q 178 " --> pdb=" O ASN Q 193 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN Q 193 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Q 187 " --> pdb=" O ASP Q 184 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 41 through 48 removed outlier: 5.789A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 129 through 132 removed outlier: 4.748A pdb=" N ALA q 130 " --> pdb=" O GLY q 6 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS q 132 " --> pdb=" O LEU q 4 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR q 177 " --> pdb=" O ARG q 19 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE q 178 " --> pdb=" O ASN q 193 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN q 193 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL q 180 " --> pdb=" O LEU q 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY q 187 " --> pdb=" O ASP q 184 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 34 through 37 removed outlier: 5.962A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA R 46 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP R 115 " --> pdb=" O ASN R 119 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN R 119 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.569A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY R 11 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL R 174 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER R 189 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG R 180 " --> pdb=" O GLY R 183 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'r' and resid 34 through 37 removed outlier: 5.961A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA r 46 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP r 115 " --> pdb=" O ASN r 119 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN r 119 " --> pdb=" O ASP r 115 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.569A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL r 174 " --> pdb=" O SER r 189 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER r 189 " --> pdb=" O VAL r 174 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG r 180 " --> pdb=" O GLY r 183 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.587A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN S 108 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY S 112 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.707A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 's' and resid 43 through 46 removed outlier: 6.587A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN s 108 " --> pdb=" O PHE s 124 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY s 112 " --> pdb=" O ALA s 120 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 's' and resid 135 through 139 removed outlier: 5.707A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'T' and resid 42 through 45 removed outlier: 4.737A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL T 130 " --> pdb=" O ASP T 126 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.405A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 't' and resid 42 through 45 removed outlier: 4.738A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL t 130 " --> pdb=" O ASP t 126 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 't' and resid 136 through 139 removed outlier: 4.404A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'g' and resid 69 through 72 removed outlier: 6.603A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL g 151 " --> pdb=" O PHE g 163 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR g 159 " --> pdb=" O ASP g 155 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 165 through 169 removed outlier: 6.127A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.565A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU h 134 " --> pdb=" O SER h 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.691A pdb=" N VAL h 44 " --> pdb=" O CYS h 213 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'i' and resid 33 through 37 removed outlier: 5.019A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE i 37 " --> pdb=" O LEU i 44 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU i 44 " --> pdb=" O ILE i 37 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'i' and resid 64 through 67 removed outlier: 6.431A pdb=" N LYS i 64 " --> pdb=" O VAL i 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL i 76 " --> pdb=" O LYS i 64 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER i 75 " --> pdb=" O LEU i 135 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) 5379 hydrogen bonds defined for protein. 16029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 47.55 Time building geometry restraints manager: 32.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 34189 1.36 - 1.51: 29206 1.51 - 1.66: 38676 1.66 - 1.80: 807 1.80 - 1.95: 173 Bond restraints: 103051 Sorted by residual: bond pdb=" O1G ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 1.491 1.950 -0.459 2.00e-02 2.50e+03 5.26e+02 bond pdb=" O1G ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 1.491 1.948 -0.457 2.00e-02 2.50e+03 5.21e+02 bond pdb=" O1G ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 1.491 1.947 -0.456 2.00e-02 2.50e+03 5.21e+02 bond pdb=" O1G ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 1.491 1.947 -0.456 2.00e-02 2.50e+03 5.19e+02 bond pdb=" C PHE U 773 " pdb=" N PRO U 774 " ideal model delta sigma weight residual 1.337 1.394 -0.058 9.80e-03 1.04e+04 3.44e+01 ... (remaining 103046 not shown) Histogram of bond angle deviations from ideal: 92.82 - 101.87: 388 101.87 - 110.92: 35154 110.92 - 119.98: 58043 119.98 - 129.03: 45210 129.03 - 138.09: 584 Bond angle restraints: 139379 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 114.42 25.45 1.00e+00 1.00e+00 6.48e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 113.13 23.70 1.00e+00 1.00e+00 5.62e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 115.11 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 118.44 21.43 1.00e+00 1.00e+00 4.59e+02 ... (remaining 139374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 59367 17.67 - 35.35: 2658 35.35 - 53.02: 542 53.02 - 70.70: 100 70.70 - 88.37: 71 Dihedral angle restraints: 62738 sinusoidal: 24840 harmonic: 37898 Sorted by residual: dihedral pdb=" N SER h 7 " pdb=" C SER h 7 " pdb=" CA SER h 7 " pdb=" CB SER h 7 " ideal model delta harmonic sigma weight residual 122.80 138.95 -16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" N SER H 7 " pdb=" C SER H 7 " pdb=" CA SER H 7 " pdb=" CB SER H 7 " ideal model delta harmonic sigma weight residual 122.80 138.51 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C SER h 7 " pdb=" N SER h 7 " pdb=" CA SER h 7 " pdb=" CB SER h 7 " ideal model delta harmonic sigma weight residual -122.60 -138.28 15.68 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 62735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 15581 0.156 - 0.312: 273 0.312 - 0.468: 16 0.468 - 0.624: 0 0.624 - 0.780: 4 Chirality restraints: 15874 Sorted by residual: chirality pdb=" CA SER h 7 " pdb=" N SER h 7 " pdb=" C SER h 7 " pdb=" CB SER h 7 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA SER H 7 " pdb=" N SER H 7 " pdb=" C SER H 7 " pdb=" CB SER H 7 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA LYS D 409 " pdb=" N LYS D 409 " pdb=" C LYS D 409 " pdb=" CB LYS D 409 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 15871 not shown) Planarity restraints: 18022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 90 " 0.093 5.00e-02 4.00e+02 1.41e-01 3.19e+01 pdb=" N PRO C 91 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 22 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.95e+01 pdb=" N PRO b 23 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO b 23 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO b 23 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 366 " 0.024 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ARG D 366 " -0.086 2.00e-02 2.50e+03 pdb=" O ARG D 366 " 0.032 2.00e-02 2.50e+03 pdb=" N PRO D 367 " 0.029 2.00e-02 2.50e+03 ... (remaining 18019 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 42 1.88 - 2.64: 2012 2.64 - 3.39: 141225 3.39 - 4.15: 253030 4.15 - 4.90: 442097 Nonbonded interactions: 838406 Sorted by model distance: nonbonded pdb=" O GLN G 127 " pdb=" CG1 VAL H 127 " model vdw 1.130 3.460 nonbonded pdb=" NH1 ARG n 91 " pdb=" O GLY n 117 " model vdw 1.195 2.520 nonbonded pdb=" NE2 HIS V 329 " pdb=" CD1 LEU V 346 " model vdw 1.276 3.540 nonbonded pdb=" CZ ARG n 91 " pdb=" O GLY n 117 " model vdw 1.279 3.270 nonbonded pdb=" O GLN g 127 " pdb=" CG1 VAL h 127 " model vdw 1.339 3.460 ... (remaining 838401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = (chain 'g' and resid 6 through 244) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 5 through 234) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 4 through 251) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 241)) selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 10.880 Check model and map are aligned: 1.100 Set scattering table: 0.710 Process input model: 260.350 Find NCS groups from input model: 6.010 Set up NCS constraints: 1.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.459 103051 Z= 0.383 Angle : 1.115 25.455 139379 Z= 0.633 Chirality : 0.060 0.780 15874 Planarity : 0.007 0.141 18022 Dihedral : 11.577 88.371 38346 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.57 % Favored : 89.91 % Rotamer: Outliers : 1.03 % Allowed : 3.79 % Favored : 95.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.06), residues: 12934 helix: -3.34 (0.04), residues: 5764 sheet: -2.17 (0.11), residues: 1748 loop : -3.06 (0.07), residues: 5422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP f 420 HIS 0.021 0.002 HIS f 301 PHE 0.042 0.003 PHE f 376 TYR 0.042 0.003 TYR V 291 ARG 0.017 0.001 ARG Y 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1368 time to evaluate : 8.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.4292 (mtp) cc_final: 0.3795 (ptt) REVERT: b 57 ASP cc_start: 0.9073 (t0) cc_final: 0.8865 (t70) REVERT: c 167 MET cc_start: 0.9046 (mtp) cc_final: 0.8253 (tmm) REVERT: c 211 GLU cc_start: 0.8990 (tp30) cc_final: 0.8776 (mp0) REVERT: c 226 MET cc_start: 0.7898 (tpp) cc_final: 0.7656 (tpt) REVERT: d 75 MET cc_start: 0.7689 (tpt) cc_final: 0.7317 (tpt) REVERT: d 112 VAL cc_start: 0.8676 (p) cc_final: 0.8408 (t) REVERT: d 116 HIS cc_start: 0.9119 (m90) cc_final: 0.8846 (m170) REVERT: d 157 ASN cc_start: 0.8516 (t0) cc_final: 0.8268 (p0) REVERT: e 67 MET cc_start: 0.3199 (mtt) cc_final: 0.2637 (mtt) REVERT: f 512 MET cc_start: 0.5281 (tpt) cc_final: 0.4978 (tpt) REVERT: U 325 MET cc_start: 0.8175 (ptm) cc_final: 0.7868 (mmp) REVERT: U 675 MET cc_start: 0.9678 (mmm) cc_final: 0.9361 (tpp) REVERT: U 766 PHE cc_start: 0.9484 (t80) cc_final: 0.9196 (t80) REVERT: V 80 LYS cc_start: 0.3475 (OUTLIER) cc_final: 0.2838 (mmmt) REVERT: V 136 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9269 (tp30) REVERT: V 235 LEU cc_start: 0.9784 (tp) cc_final: 0.9467 (mt) REVERT: V 301 GLU cc_start: 0.9182 (tp30) cc_final: 0.8652 (tm-30) REVERT: W 16 MET cc_start: 0.8512 (mmt) cc_final: 0.7492 (mmt) REVERT: W 80 TRP cc_start: 0.9359 (t-100) cc_final: 0.9041 (t60) REVERT: W 88 MET cc_start: 0.6871 (mtm) cc_final: 0.6529 (mtm) REVERT: W 130 MET cc_start: 0.8727 (mpt) cc_final: 0.8416 (pmm) REVERT: W 417 ARG cc_start: 0.7120 (ppt-90) cc_final: 0.6870 (mpt180) REVERT: X 78 ASN cc_start: 0.9668 (t0) cc_final: 0.9343 (m110) REVERT: X 216 ILE cc_start: 0.9718 (OUTLIER) cc_final: 0.9479 (mm) REVERT: X 415 TYR cc_start: 0.9177 (m-80) cc_final: 0.8894 (p90) REVERT: Y 73 MET cc_start: 0.7590 (mtp) cc_final: 0.7172 (ttm) REVERT: Y 104 MET cc_start: 0.9521 (tpp) cc_final: 0.8776 (mmm) REVERT: Y 302 HIS cc_start: 0.9188 (t70) cc_final: 0.8714 (t70) REVERT: Y 382 LYS cc_start: 0.9693 (ttpp) cc_final: 0.9428 (tptm) REVERT: A 156 LYS cc_start: 0.9456 (tttt) cc_final: 0.9043 (tptp) REVERT: A 164 MET cc_start: 0.8706 (ptp) cc_final: 0.8371 (mpp) REVERT: A 319 MET cc_start: 0.9620 (mtt) cc_final: 0.9327 (tmm) REVERT: A 362 MET cc_start: 0.8934 (ptm) cc_final: 0.8459 (ptt) REVERT: B 269 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8843 (pp20) REVERT: B 271 PHE cc_start: 0.9293 (m-80) cc_final: 0.9041 (m-80) REVERT: B 405 MET cc_start: 0.9643 (mmm) cc_final: 0.9059 (mtp) REVERT: C 124 HIS cc_start: 0.8914 (t70) cc_final: 0.8422 (t-90) REVERT: C 383 PHE cc_start: 0.9293 (m-80) cc_final: 0.8960 (m-80) REVERT: D 151 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8392 (tt) REVERT: D 242 GLU cc_start: 0.9207 (tt0) cc_final: 0.9001 (pm20) REVERT: D 296 MET cc_start: 0.7847 (tpt) cc_final: 0.7553 (tpt) REVERT: D 369 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6630 (pttm) REVERT: D 412 GLN cc_start: 0.6070 (OUTLIER) cc_final: 0.5845 (pp30) REVERT: D 415 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6250 (tp30) REVERT: F 206 MET cc_start: 0.9404 (tmt) cc_final: 0.9156 (ptm) REVERT: G 93 ARG cc_start: 0.9874 (mmm-85) cc_final: 0.9626 (mmm160) REVERT: G 138 MET cc_start: 0.9280 (ttm) cc_final: 0.9052 (ptp) REVERT: H 51 LYS cc_start: 0.7498 (mtpp) cc_final: 0.7153 (mmtp) REVERT: H 70 LYS cc_start: 0.9620 (ptpt) cc_final: 0.9408 (tptt) REVERT: J 38 ARG cc_start: 0.9473 (ttt180) cc_final: 0.9007 (mmp-170) REVERT: J 65 LEU cc_start: 0.9700 (mt) cc_final: 0.9400 (mt) REVERT: K 21 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7286 (tp) REVERT: K 31 ILE cc_start: 0.8967 (mt) cc_final: 0.8746 (mm) REVERT: K 118 ASN cc_start: 0.9599 (m-40) cc_final: 0.9353 (m110) REVERT: K 143 PHE cc_start: 0.8636 (m-10) cc_final: 0.8296 (m-80) REVERT: K 156 MET cc_start: 0.8394 (ptm) cc_final: 0.7777 (ttp) REVERT: L 6 TYR cc_start: 0.8513 (p90) cc_final: 0.8180 (p90) REVERT: L 88 MET cc_start: 0.9578 (tpp) cc_final: 0.9271 (tpp) REVERT: L 153 TYR cc_start: 0.8897 (p90) cc_final: 0.8445 (p90) REVERT: L 159 MET cc_start: 0.8232 (mmm) cc_final: 0.7438 (mmt) REVERT: L 172 LEU cc_start: 0.9761 (mt) cc_final: 0.9513 (tp) REVERT: M 27 MET cc_start: 0.8803 (mtt) cc_final: 0.8381 (mmt) REVERT: M 67 PHE cc_start: 0.7901 (m-10) cc_final: 0.7588 (m-10) REVERT: M 75 MET cc_start: 0.9349 (mtp) cc_final: 0.8788 (mmp) REVERT: M 135 PHE cc_start: 0.9414 (p90) cc_final: 0.9180 (p90) REVERT: N 33 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8748 (mmmm) REVERT: O 24 MET cc_start: 0.9318 (mmm) cc_final: 0.9006 (tmm) REVERT: O 83 LEU cc_start: 0.9873 (mt) cc_final: 0.9503 (pp) REVERT: O 93 TYR cc_start: 0.9255 (m-10) cc_final: 0.8982 (m-10) REVERT: P 117 PHE cc_start: 0.9209 (p90) cc_final: 0.8899 (p90) REVERT: P 131 MET cc_start: 0.8532 (ttp) cc_final: 0.8270 (tmm) REVERT: Q 69 MET cc_start: 0.8974 (mmm) cc_final: 0.8701 (mmt) REVERT: R 86 MET cc_start: 0.9553 (mtm) cc_final: 0.8837 (ptm) REVERT: R 175 ASN cc_start: 0.8406 (m-40) cc_final: 0.7917 (m110) REVERT: S 107 TYR cc_start: 0.9757 (m-80) cc_final: 0.9502 (m-10) REVERT: T 5 MET cc_start: 0.9420 (mmt) cc_final: 0.9204 (mmm) REVERT: T 22 ILE cc_start: 0.9214 (mt) cc_final: 0.8499 (mp) REVERT: T 51 LEU cc_start: 0.9591 (tp) cc_final: 0.9384 (tp) REVERT: T 96 MET cc_start: 0.9721 (mmm) cc_final: 0.8476 (tpt) REVERT: T 112 ILE cc_start: 0.9574 (mt) cc_final: 0.9165 (tt) REVERT: T 127 MET cc_start: 0.7854 (ttp) cc_final: 0.6709 (ttm) REVERT: T 173 MET cc_start: 0.9685 (mmm) cc_final: 0.9334 (tpp) REVERT: g 19 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9121 (pp20) REVERT: g 134 LEU cc_start: 0.9291 (mt) cc_final: 0.9075 (tp) REVERT: h 22 ILE cc_start: 0.9206 (mt) cc_final: 0.8860 (mp) REVERT: h 130 PHE cc_start: 0.8637 (m-80) cc_final: 0.8133 (m-80) REVERT: h 156 PHE cc_start: 0.9607 (m-80) cc_final: 0.8914 (m-80) REVERT: i 26 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9230 (mt-10) REVERT: i 67 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8767 (tptm) REVERT: i 71 ASP cc_start: 0.7964 (p0) cc_final: 0.7564 (m-30) REVERT: i 72 MET cc_start: 0.8623 (mtm) cc_final: 0.8234 (mpp) REVERT: i 117 ILE cc_start: 0.9783 (mt) cc_final: 0.9471 (mt) REVERT: i 174 MET cc_start: 0.9446 (ttm) cc_final: 0.9188 (ttm) REVERT: j 56 GLU cc_start: 0.9247 (pm20) cc_final: 0.8943 (mp0) REVERT: j 71 MET cc_start: 0.9460 (mmp) cc_final: 0.9246 (mmm) REVERT: j 96 LEU cc_start: 0.9568 (tt) cc_final: 0.9289 (mt) REVERT: j 106 TYR cc_start: 0.9602 (t80) cc_final: 0.9277 (t80) REVERT: k 78 MET cc_start: 0.9156 (ptp) cc_final: 0.8830 (ptp) REVERT: k 90 ASP cc_start: 0.9453 (t0) cc_final: 0.9089 (p0) REVERT: k 107 MET cc_start: 0.8286 (ttm) cc_final: 0.7873 (ttm) REVERT: k 112 VAL cc_start: 0.9794 (t) cc_final: 0.9307 (t) REVERT: k 143 PHE cc_start: 0.9381 (m-10) cc_final: 0.9006 (m-80) REVERT: k 156 MET cc_start: 0.9156 (ptm) cc_final: 0.8643 (ttp) REVERT: l 26 MET cc_start: 0.9111 (mmt) cc_final: 0.8904 (mmt) REVERT: l 64 LEU cc_start: 0.9703 (pp) cc_final: 0.9482 (pp) REVERT: l 86 ASN cc_start: 0.9485 (m-40) cc_final: 0.9248 (p0) REVERT: m 19 ARG cc_start: 0.9588 (ptt-90) cc_final: 0.9333 (mtm110) REVERT: n 4 MET cc_start: 0.9664 (ttt) cc_final: 0.9224 (tmm) REVERT: n 14 LEU cc_start: 0.9590 (mp) cc_final: 0.9067 (tp) REVERT: n 32 ASP cc_start: 0.9537 (m-30) cc_final: 0.8962 (t0) REVERT: n 84 LYS cc_start: 0.9656 (ttpp) cc_final: 0.9349 (ttmm) REVERT: n 116 MET cc_start: 0.8920 (mtp) cc_final: 0.8391 (tpt) REVERT: o 54 MET cc_start: 0.9788 (mmm) cc_final: 0.9515 (mmm) REVERT: o 82 MET cc_start: 0.9331 (mtt) cc_final: 0.8903 (mmt) REVERT: o 93 TYR cc_start: 0.8719 (m-10) cc_final: 0.8394 (m-80) REVERT: p 6 TYR cc_start: 0.9096 (t80) cc_final: 0.8841 (t80) REVERT: p 12 MET cc_start: 0.8669 (ttm) cc_final: 0.7676 (tpt) REVERT: p 14 MET cc_start: 0.9545 (ttm) cc_final: 0.8938 (tpp) REVERT: p 149 MET cc_start: 0.8966 (mmm) cc_final: 0.8702 (mmp) REVERT: p 171 MET cc_start: 0.9610 (mmm) cc_final: 0.9368 (mmm) REVERT: q 36 PHE cc_start: 0.8844 (m-10) cc_final: 0.8396 (m-80) REVERT: q 58 GLU cc_start: 0.9650 (mt-10) cc_final: 0.9329 (tp30) REVERT: q 88 LEU cc_start: 0.9221 (mp) cc_final: 0.8800 (mp) REVERT: q 167 LEU cc_start: 0.9687 (tt) cc_final: 0.9384 (mt) REVERT: r 32 LYS cc_start: 0.9428 (mtpt) cc_final: 0.9222 (ttpp) REVERT: r 93 MET cc_start: 0.9647 (mtt) cc_final: 0.9284 (mtt) REVERT: r 117 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9424 (tm-30) REVERT: r 139 MET cc_start: 0.9536 (ttp) cc_final: 0.9058 (tmm) REVERT: t 5 MET cc_start: 0.9527 (mmt) cc_final: 0.9284 (mmm) REVERT: t 22 ILE cc_start: 0.9699 (mt) cc_final: 0.9163 (mp) REVERT: t 26 MET cc_start: 0.8651 (mtp) cc_final: 0.8375 (mmm) REVERT: t 60 PHE cc_start: 0.9303 (t80) cc_final: 0.8985 (t80) REVERT: t 62 TYR cc_start: 0.9813 (t80) cc_final: 0.9543 (t80) REVERT: t 96 MET cc_start: 0.9743 (mmm) cc_final: 0.8954 (tpt) REVERT: t 127 MET cc_start: 0.6996 (ttp) cc_final: 0.6054 (ttm) outliers start: 110 outliers final: 51 residues processed: 1470 average time/residue: 0.9643 time to fit residues: 2374.8228 Evaluate side-chains 840 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 781 time to evaluate : 8.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1087 optimal weight: 7.9990 chunk 976 optimal weight: 4.9990 chunk 541 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 658 optimal weight: 8.9990 chunk 521 optimal weight: 2.9990 chunk 1009 optimal weight: 40.0000 chunk 390 optimal weight: 5.9990 chunk 613 optimal weight: 6.9990 chunk 751 optimal weight: 5.9990 chunk 1169 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 GLN a 249 GLN b 76 HIS c 149 GLN c 190 GLN c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 HIS ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 180 GLN f 405 HIS ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 473 ASN f 475 ASN f 540 GLN f 747 GLN U 18 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 596 ASN ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 777 HIS U 880 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 ASN V 118 GLN V 146 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 282 ASN V 453 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 HIS Y 136 HIS ** Y 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN Z 229 GLN Z 243 GLN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 332 ASN C 36 ASN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 332 HIS D 74 HIS D 133 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN E 323 HIS F 218 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 GLN N 66 HIS O 62 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 119 ASN T 2 GLN T 69 GLN T 188 GLN g 127 GLN h 88 HIS h 123 GLN ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 ASN ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 ASN k 114 GLN k 118 ASN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 110 HIS n 28 ASN n 62 GLN n 66 HIS ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 ASN ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 173 ASN q 27 GLN q 65 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN q 101 ASN q 168 GLN r 38 ASN r 119 ASN t 2 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 103051 Z= 0.240 Angle : 0.753 14.212 139379 Z= 0.396 Chirality : 0.045 0.361 15874 Planarity : 0.006 0.141 18022 Dihedral : 7.678 88.380 14347 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.56 % Rotamer: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.07), residues: 12934 helix: -1.65 (0.06), residues: 5883 sheet: -1.85 (0.11), residues: 1782 loop : -2.71 (0.08), residues: 5269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 43 HIS 0.019 0.001 HIS V 329 PHE 0.036 0.002 PHE f 304 TYR 0.031 0.002 TYR G 125 ARG 0.016 0.001 ARG n 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 921 time to evaluate : 8.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.4294 (mtp) cc_final: 0.3512 (ptt) REVERT: a 280 MET cc_start: 0.8674 (ptp) cc_final: 0.8439 (ptp) REVERT: b 7 MET cc_start: 0.5793 (tpp) cc_final: 0.5545 (tpp) REVERT: c 167 MET cc_start: 0.8908 (mtp) cc_final: 0.8181 (tmm) REVERT: c 168 MET cc_start: 0.7911 (tmm) cc_final: 0.7642 (tmm) REVERT: c 226 MET cc_start: 0.8126 (tpp) cc_final: 0.7920 (tpt) REVERT: c 292 MET cc_start: 0.9438 (mmp) cc_final: 0.9152 (mmp) REVERT: d 75 MET cc_start: 0.8180 (tpt) cc_final: 0.7707 (tpt) REVERT: d 116 HIS cc_start: 0.9094 (m90) cc_final: 0.8782 (m170) REVERT: e 67 MET cc_start: 0.3253 (mtt) cc_final: 0.2612 (mtt) REVERT: f 209 MET cc_start: 0.7525 (ppp) cc_final: 0.5234 (mmt) REVERT: f 340 MET cc_start: 0.6503 (ptt) cc_final: 0.6165 (ptp) REVERT: U 137 MET cc_start: 0.8985 (mmp) cc_final: 0.8565 (mmt) REVERT: U 188 MET cc_start: 0.4849 (ttm) cc_final: 0.4643 (ttm) REVERT: U 325 MET cc_start: 0.8142 (ptm) cc_final: 0.7824 (mmp) REVERT: U 333 MET cc_start: 0.9445 (ppp) cc_final: 0.9217 (ppp) REVERT: U 675 MET cc_start: 0.9694 (mmm) cc_final: 0.9368 (tpp) REVERT: U 766 PHE cc_start: 0.9564 (t80) cc_final: 0.9275 (t80) REVERT: U 880 ASN cc_start: 0.5345 (OUTLIER) cc_final: 0.4825 (p0) REVERT: U 894 MET cc_start: 0.8387 (ttt) cc_final: 0.7696 (tmm) REVERT: V 37 MET cc_start: 0.8574 (mmm) cc_final: 0.8279 (mmm) REVERT: W 16 MET cc_start: 0.8629 (mmt) cc_final: 0.7886 (mmt) REVERT: W 130 MET cc_start: 0.8769 (mpp) cc_final: 0.8153 (pmm) REVERT: W 177 MET cc_start: 0.7523 (tpt) cc_final: 0.6563 (mmm) REVERT: W 378 MET cc_start: 0.9201 (ttm) cc_final: 0.8942 (tpp) REVERT: W 451 MET cc_start: 0.8307 (mmp) cc_final: 0.8063 (mmp) REVERT: X 78 ASN cc_start: 0.9642 (t0) cc_final: 0.9278 (m110) REVERT: Y 73 MET cc_start: 0.8206 (mtp) cc_final: 0.7770 (ttm) REVERT: Y 104 MET cc_start: 0.9559 (tpp) cc_final: 0.8830 (mmt) REVERT: Y 282 MET cc_start: 0.7998 (mmt) cc_final: 0.7468 (mmt) REVERT: Y 302 HIS cc_start: 0.9130 (t70) cc_final: 0.8671 (t70) REVERT: Z 78 MET cc_start: 0.9115 (tpp) cc_final: 0.8837 (tpp) REVERT: A 156 LYS cc_start: 0.9482 (tttt) cc_final: 0.9071 (tptp) REVERT: A 263 MET cc_start: 0.9525 (tpt) cc_final: 0.9071 (tpp) REVERT: B 192 ASN cc_start: 0.9657 (t0) cc_final: 0.9419 (p0) REVERT: B 329 MET cc_start: 0.8698 (ppp) cc_final: 0.8375 (ppp) REVERT: B 405 MET cc_start: 0.9625 (mmm) cc_final: 0.9020 (mtp) REVERT: C 124 HIS cc_start: 0.8994 (t70) cc_final: 0.8514 (t-90) REVERT: C 293 MET cc_start: 0.7746 (tmm) cc_final: 0.7318 (tmm) REVERT: C 351 MET cc_start: 0.7553 (mtt) cc_final: 0.6644 (ttt) REVERT: C 391 MET cc_start: 0.9518 (tpt) cc_final: 0.9295 (mmm) REVERT: D 149 SER cc_start: 0.6301 (p) cc_final: 0.5940 (m) REVERT: D 214 MET cc_start: 0.9265 (ptp) cc_final: 0.8907 (ptp) REVERT: D 296 MET cc_start: 0.8167 (tpt) cc_final: 0.7779 (tpt) REVERT: E 102 MET cc_start: 0.9596 (pmm) cc_final: 0.9215 (mpp) REVERT: E 352 MET cc_start: 0.9294 (tmm) cc_final: 0.8663 (tmm) REVERT: G 19 GLU cc_start: 0.9683 (pm20) cc_final: 0.9411 (mp0) REVERT: G 103 TYR cc_start: 0.9545 (t80) cc_final: 0.9282 (t80) REVERT: G 125 TYR cc_start: 0.9712 (m-80) cc_final: 0.9456 (m-80) REVERT: G 131 MET cc_start: 0.4634 (ppp) cc_final: 0.4366 (ppp) REVERT: G 138 MET cc_start: 0.9335 (ttm) cc_final: 0.8937 (tpp) REVERT: H 121 TYR cc_start: 0.9546 (m-80) cc_final: 0.9252 (m-80) REVERT: I 45 LEU cc_start: 0.9853 (mt) cc_final: 0.9620 (tp) REVERT: J 133 ILE cc_start: 0.9399 (tp) cc_final: 0.9156 (tp) REVERT: K 59 MET cc_start: 0.8442 (ttt) cc_final: 0.7901 (ttt) REVERT: K 143 PHE cc_start: 0.8688 (m-10) cc_final: 0.8460 (m-10) REVERT: K 156 MET cc_start: 0.8632 (ptm) cc_final: 0.8396 (ttp) REVERT: K 189 MET cc_start: 0.7001 (mmt) cc_final: 0.6652 (mmm) REVERT: K 228 MET cc_start: 0.7893 (pmm) cc_final: 0.7644 (pmm) REVERT: L 6 TYR cc_start: 0.8273 (p90) cc_final: 0.7529 (p90) REVERT: L 108 LEU cc_start: 0.9712 (tt) cc_final: 0.9388 (mp) REVERT: L 153 TYR cc_start: 0.8979 (p90) cc_final: 0.8496 (p90) REVERT: L 159 MET cc_start: 0.8625 (mmm) cc_final: 0.8157 (mmt) REVERT: L 176 MET cc_start: 0.9460 (ptp) cc_final: 0.8994 (ptp) REVERT: M 27 MET cc_start: 0.8899 (mtt) cc_final: 0.8540 (mmt) REVERT: M 67 PHE cc_start: 0.7916 (m-10) cc_final: 0.7649 (m-10) REVERT: M 75 MET cc_start: 0.9382 (mtp) cc_final: 0.9155 (mmp) REVERT: M 135 PHE cc_start: 0.9545 (p90) cc_final: 0.8068 (p90) REVERT: M 137 LEU cc_start: 0.9329 (mt) cc_final: 0.8930 (mt) REVERT: M 181 MET cc_start: 0.6707 (ptm) cc_final: 0.6352 (ptm) REVERT: M 184 MET cc_start: 0.8271 (mtm) cc_final: 0.7815 (ttp) REVERT: N 33 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8808 (mmmm) REVERT: N 85 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9196 (mt-10) REVERT: N 95 MET cc_start: 0.9289 (mpp) cc_final: 0.8977 (mpp) REVERT: O 24 MET cc_start: 0.9243 (mmm) cc_final: 0.9019 (tmm) REVERT: O 54 MET cc_start: 0.9506 (mpp) cc_final: 0.9190 (mpp) REVERT: O 93 TYR cc_start: 0.9284 (m-10) cc_final: 0.9030 (m-10) REVERT: P 14 MET cc_start: 0.9631 (ttm) cc_final: 0.9092 (tpp) REVERT: P 96 TYR cc_start: 0.9785 (t80) cc_final: 0.9335 (t80) REVERT: P 117 PHE cc_start: 0.9210 (p90) cc_final: 0.8925 (p90) REVERT: P 131 MET cc_start: 0.8574 (ttp) cc_final: 0.8288 (tmm) REVERT: P 144 GLU cc_start: 0.9713 (pm20) cc_final: 0.9201 (tt0) REVERT: Q 44 LEU cc_start: 0.9691 (tp) cc_final: 0.9372 (tp) REVERT: Q 69 MET cc_start: 0.9065 (mmm) cc_final: 0.8654 (tpt) REVERT: R 86 MET cc_start: 0.9613 (mtm) cc_final: 0.9087 (mtp) REVERT: R 100 MET cc_start: 0.9270 (mtt) cc_final: 0.8087 (tpp) REVERT: R 175 ASN cc_start: 0.8195 (m-40) cc_final: 0.7885 (m110) REVERT: T 26 MET cc_start: 0.8663 (mmp) cc_final: 0.7834 (mmm) REVERT: T 43 MET cc_start: 0.9067 (tmm) cc_final: 0.8800 (tmm) REVERT: T 51 LEU cc_start: 0.9792 (tp) cc_final: 0.9499 (tp) REVERT: T 96 MET cc_start: 0.9607 (mmm) cc_final: 0.8486 (tpt) REVERT: T 127 MET cc_start: 0.7840 (ttp) cc_final: 0.6499 (ttm) REVERT: T 173 MET cc_start: 0.9715 (mmm) cc_final: 0.9276 (tpp) REVERT: T 214 MET cc_start: 0.9441 (mpp) cc_final: 0.9154 (mpp) REVERT: g 134 LEU cc_start: 0.9422 (mt) cc_final: 0.9084 (tp) REVERT: h 113 ARG cc_start: 0.9537 (mtt-85) cc_final: 0.9094 (mtm180) REVERT: h 130 PHE cc_start: 0.8644 (m-80) cc_final: 0.8088 (m-80) REVERT: i 26 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9328 (mt-10) REVERT: i 71 ASP cc_start: 0.7872 (p0) cc_final: 0.7506 (m-30) REVERT: i 174 MET cc_start: 0.9396 (ttm) cc_final: 0.9153 (ttm) REVERT: j 21 TYR cc_start: 0.9154 (m-10) cc_final: 0.8954 (m-80) REVERT: j 106 TYR cc_start: 0.9641 (t80) cc_final: 0.9369 (t80) REVERT: j 132 LEU cc_start: 0.9532 (mt) cc_final: 0.9303 (mp) REVERT: k 78 MET cc_start: 0.9182 (ptp) cc_final: 0.8632 (ppp) REVERT: k 90 ASP cc_start: 0.9434 (t0) cc_final: 0.9178 (p0) REVERT: k 107 MET cc_start: 0.8212 (ttm) cc_final: 0.7667 (ttm) REVERT: k 143 PHE cc_start: 0.9369 (m-10) cc_final: 0.9078 (m-80) REVERT: k 156 MET cc_start: 0.9269 (ptm) cc_final: 0.8584 (ttp) REVERT: l 26 MET cc_start: 0.9465 (mmt) cc_final: 0.8884 (mmt) REVERT: l 115 LYS cc_start: 0.9531 (tptp) cc_final: 0.9243 (mmmm) REVERT: m 47 PHE cc_start: 0.9574 (m-10) cc_final: 0.9062 (m-10) REVERT: m 75 MET cc_start: 0.9498 (mpp) cc_final: 0.9052 (mpp) REVERT: m 150 MET cc_start: 0.9537 (tmm) cc_final: 0.9209 (ppp) REVERT: n 4 MET cc_start: 0.9684 (ttt) cc_final: 0.9208 (tmm) REVERT: n 14 LEU cc_start: 0.9607 (mp) cc_final: 0.9160 (tp) REVERT: n 86 MET cc_start: 0.9304 (tpt) cc_final: 0.8879 (mmm) REVERT: o 54 MET cc_start: 0.9793 (mmm) cc_final: 0.9477 (mmp) REVERT: o 82 MET cc_start: 0.9312 (mtt) cc_final: 0.9069 (mmm) REVERT: o 87 LEU cc_start: 0.9713 (mt) cc_final: 0.9162 (mt) REVERT: o 93 TYR cc_start: 0.8803 (m-10) cc_final: 0.8489 (m-10) REVERT: o 127 MET cc_start: 0.8312 (mmt) cc_final: 0.7558 (mtt) REVERT: o 146 MET cc_start: 0.8814 (mtt) cc_final: 0.8526 (mtt) REVERT: p 14 MET cc_start: 0.9403 (ttm) cc_final: 0.9025 (ttm) REVERT: p 171 MET cc_start: 0.9588 (mmm) cc_final: 0.9336 (mmm) REVERT: q 36 PHE cc_start: 0.8830 (m-10) cc_final: 0.8391 (m-80) REVERT: q 118 MET cc_start: 0.7604 (tpp) cc_final: 0.7339 (tpp) REVERT: q 167 LEU cc_start: 0.9758 (tt) cc_final: 0.9451 (mt) REVERT: r 45 MET cc_start: 0.8746 (ttt) cc_final: 0.8524 (tpp) REVERT: r 82 LEU cc_start: 0.9872 (tt) cc_final: 0.9625 (tt) REVERT: r 86 MET cc_start: 0.9545 (mmp) cc_final: 0.9296 (mmp) REVERT: r 93 MET cc_start: 0.9540 (mtt) cc_final: 0.9323 (mtt) REVERT: r 100 MET cc_start: 0.9293 (mtt) cc_final: 0.8662 (tpp) REVERT: r 117 GLU cc_start: 0.9702 (mm-30) cc_final: 0.9428 (tm-30) REVERT: r 139 MET cc_start: 0.9587 (ttp) cc_final: 0.9126 (ptt) REVERT: t 12 LEU cc_start: 0.9840 (mt) cc_final: 0.9614 (pp) REVERT: t 60 PHE cc_start: 0.9243 (t80) cc_final: 0.8899 (t80) REVERT: t 62 TYR cc_start: 0.9814 (t80) cc_final: 0.9595 (t80) REVERT: t 70 MET cc_start: 0.9776 (mtm) cc_final: 0.9524 (ptp) REVERT: t 96 MET cc_start: 0.9732 (mmm) cc_final: 0.8976 (tpt) REVERT: t 127 MET cc_start: 0.7017 (ttp) cc_final: 0.5963 (ttm) REVERT: t 173 MET cc_start: 0.9431 (mtp) cc_final: 0.9096 (ttm) outliers start: 21 outliers final: 8 residues processed: 940 average time/residue: 0.9799 time to fit residues: 1580.0099 Evaluate side-chains 707 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 698 time to evaluate : 8.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 650 optimal weight: 20.0000 chunk 363 optimal weight: 0.5980 chunk 973 optimal weight: 20.0000 chunk 796 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 1171 optimal weight: 10.0000 chunk 1265 optimal weight: 9.9990 chunk 1043 optimal weight: 6.9990 chunk 1161 optimal weight: 3.9990 chunk 399 optimal weight: 7.9990 chunk 940 optimal weight: 0.2980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN c 101 GLN c 210 ASN c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 GLN ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 178 HIS X 322 HIS ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 314 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN D 412 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 83 ASN F 218 GLN F 258 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 110 HIS ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN r 38 ASN t 69 GLN ** t 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 103051 Z= 0.193 Angle : 0.693 15.478 139379 Z= 0.360 Chirality : 0.045 0.300 15874 Planarity : 0.005 0.128 18022 Dihedral : 7.210 84.164 14347 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.57 % Favored : 91.28 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 12934 helix: -0.84 (0.06), residues: 5966 sheet: -1.59 (0.11), residues: 1806 loop : -2.52 (0.08), residues: 5162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP W 80 HIS 0.013 0.001 HIS f 301 PHE 0.036 0.002 PHE f 304 TYR 0.038 0.002 TYR g 125 ARG 0.013 0.001 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 828 time to evaluate : 10.578 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3988 (mtp) cc_final: 0.3176 (ptt) REVERT: a 280 MET cc_start: 0.8406 (ptp) cc_final: 0.8097 (ptp) REVERT: b 7 MET cc_start: 0.5859 (tpp) cc_final: 0.5606 (tpp) REVERT: c 75 MET cc_start: 0.7925 (tmm) cc_final: 0.7721 (tmm) REVERT: c 95 MET cc_start: 0.9736 (tpp) cc_final: 0.9066 (mmm) REVERT: c 167 MET cc_start: 0.8927 (mtp) cc_final: 0.8220 (tmm) REVERT: c 168 MET cc_start: 0.7814 (tmm) cc_final: 0.7520 (tmm) REVERT: d 75 MET cc_start: 0.8309 (tpt) cc_final: 0.8092 (tpt) REVERT: d 116 HIS cc_start: 0.9074 (m90) cc_final: 0.8707 (m170) REVERT: e 67 MET cc_start: 0.3551 (mtt) cc_final: 0.3070 (mtt) REVERT: f 133 MET cc_start: 0.6199 (mtt) cc_final: 0.5748 (mtt) REVERT: f 209 MET cc_start: 0.7415 (ppp) cc_final: 0.5102 (mmt) REVERT: f 340 MET cc_start: 0.6369 (ptt) cc_final: 0.5567 (ptp) REVERT: U 188 MET cc_start: 0.5112 (ttm) cc_final: 0.4826 (ttm) REVERT: U 325 MET cc_start: 0.8261 (ptm) cc_final: 0.7967 (mmp) REVERT: U 333 MET cc_start: 0.9466 (ppp) cc_final: 0.9254 (ppp) REVERT: U 423 MET cc_start: 0.9268 (mpp) cc_final: 0.8274 (ppp) REVERT: U 675 MET cc_start: 0.9723 (mmm) cc_final: 0.9408 (tpp) REVERT: U 766 PHE cc_start: 0.9602 (t80) cc_final: 0.9327 (t80) REVERT: U 894 MET cc_start: 0.8270 (ttt) cc_final: 0.7714 (tmm) REVERT: V 37 MET cc_start: 0.8788 (mmm) cc_final: 0.8148 (mmm) REVERT: V 409 MET cc_start: 0.9216 (ptp) cc_final: 0.8855 (ppp) REVERT: W 16 MET cc_start: 0.8598 (mmt) cc_final: 0.7817 (mmt) REVERT: W 88 MET cc_start: 0.6105 (mtp) cc_final: 0.5751 (mtm) REVERT: W 130 MET cc_start: 0.8919 (mpp) cc_final: 0.8647 (mpp) REVERT: W 177 MET cc_start: 0.7618 (tpt) cc_final: 0.6708 (mmm) REVERT: W 451 MET cc_start: 0.8363 (mmp) cc_final: 0.8159 (mmp) REVERT: X 78 ASN cc_start: 0.9648 (t0) cc_final: 0.9280 (m110) REVERT: Y 73 MET cc_start: 0.8175 (mtp) cc_final: 0.7799 (ttm) REVERT: Y 104 MET cc_start: 0.9540 (tpp) cc_final: 0.9292 (tpp) REVERT: Y 282 MET cc_start: 0.8130 (mmt) cc_final: 0.7916 (mmt) REVERT: Y 302 HIS cc_start: 0.9087 (t70) cc_final: 0.8601 (t70) REVERT: Z 78 MET cc_start: 0.9343 (tpp) cc_final: 0.8701 (tpp) REVERT: A 156 LYS cc_start: 0.9462 (tttt) cc_final: 0.9105 (tmtt) REVERT: A 256 MET cc_start: 0.9425 (mmp) cc_final: 0.9069 (mmm) REVERT: A 263 MET cc_start: 0.9462 (tpt) cc_final: 0.9017 (tpp) REVERT: B 192 ASN cc_start: 0.9693 (t0) cc_final: 0.9452 (p0) REVERT: B 271 PHE cc_start: 0.9480 (m-80) cc_final: 0.9254 (m-80) REVERT: B 329 MET cc_start: 0.8776 (ppp) cc_final: 0.8490 (ppp) REVERT: B 405 MET cc_start: 0.9628 (mmm) cc_final: 0.9087 (mtp) REVERT: B 428 TYR cc_start: 0.9641 (m-80) cc_final: 0.9238 (m-80) REVERT: C 124 HIS cc_start: 0.9008 (t70) cc_final: 0.8479 (t-90) REVERT: C 351 MET cc_start: 0.7563 (mtt) cc_final: 0.6670 (ttm) REVERT: C 391 MET cc_start: 0.9546 (tpt) cc_final: 0.9321 (mmm) REVERT: D 214 MET cc_start: 0.9308 (ptp) cc_final: 0.9068 (ptm) REVERT: D 284 GLU cc_start: 0.9505 (mp0) cc_final: 0.9156 (tp30) REVERT: D 296 MET cc_start: 0.8469 (tpt) cc_final: 0.8190 (tpt) REVERT: D 352 MET cc_start: 0.6720 (mpp) cc_final: 0.6336 (mpp) REVERT: D 412 GLN cc_start: 0.4588 (OUTLIER) cc_final: 0.4376 (pp30) REVERT: E 102 MET cc_start: 0.9598 (pmm) cc_final: 0.9207 (mpp) REVERT: E 232 MET cc_start: 0.9527 (tmm) cc_final: 0.9177 (tmm) REVERT: E 352 MET cc_start: 0.9354 (tmm) cc_final: 0.8910 (tmm) REVERT: F 336 ASP cc_start: 0.9512 (p0) cc_final: 0.9198 (p0) REVERT: G 19 GLU cc_start: 0.9650 (pm20) cc_final: 0.9425 (mp0) REVERT: G 83 MET cc_start: 0.9399 (mmp) cc_final: 0.9047 (mmm) REVERT: G 103 TYR cc_start: 0.9529 (t80) cc_final: 0.9252 (t80) REVERT: G 138 MET cc_start: 0.9303 (ttm) cc_final: 0.8894 (tpp) REVERT: H 121 TYR cc_start: 0.9589 (m-80) cc_final: 0.9306 (m-80) REVERT: J 38 ARG cc_start: 0.9526 (ttt180) cc_final: 0.9109 (mmp-170) REVERT: J 65 LEU cc_start: 0.9672 (mt) cc_final: 0.9254 (mp) REVERT: K 59 MET cc_start: 0.8653 (ttt) cc_final: 0.8018 (ttt) REVERT: K 228 MET cc_start: 0.7986 (pmm) cc_final: 0.7641 (pmm) REVERT: L 41 LYS cc_start: 0.9557 (mmmm) cc_final: 0.9308 (mmmt) REVERT: L 88 MET cc_start: 0.9850 (mtm) cc_final: 0.9459 (ptt) REVERT: L 108 LEU cc_start: 0.9688 (tt) cc_final: 0.9445 (mp) REVERT: L 153 TYR cc_start: 0.8991 (p90) cc_final: 0.8517 (p90) REVERT: L 159 MET cc_start: 0.7786 (mmm) cc_final: 0.7087 (mmt) REVERT: M 27 MET cc_start: 0.8957 (mtt) cc_final: 0.8574 (mmt) REVERT: M 47 PHE cc_start: 0.8888 (m-10) cc_final: 0.8587 (m-10) REVERT: M 67 PHE cc_start: 0.7882 (m-10) cc_final: 0.7554 (m-10) REVERT: M 75 MET cc_start: 0.9358 (mtp) cc_final: 0.8715 (mmt) REVERT: M 135 PHE cc_start: 0.9545 (p90) cc_final: 0.9125 (p90) REVERT: M 136 MET cc_start: 0.9358 (mmp) cc_final: 0.8912 (mtt) REVERT: M 181 MET cc_start: 0.6483 (ptm) cc_final: 0.6220 (ptm) REVERT: N 33 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8992 (mmmm) REVERT: N 51 ASP cc_start: 0.9564 (m-30) cc_final: 0.9113 (t0) REVERT: N 85 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9098 (mt-10) REVERT: N 119 MET cc_start: 0.9029 (mmt) cc_final: 0.7470 (tpp) REVERT: O 54 MET cc_start: 0.9504 (mpp) cc_final: 0.9063 (mpp) REVERT: O 93 TYR cc_start: 0.9290 (m-10) cc_final: 0.9028 (m-10) REVERT: P 14 MET cc_start: 0.9563 (ttm) cc_final: 0.8823 (ttm) REVERT: P 96 TYR cc_start: 0.9784 (t80) cc_final: 0.9301 (t80) REVERT: P 117 PHE cc_start: 0.9205 (p90) cc_final: 0.8923 (p90) REVERT: P 144 GLU cc_start: 0.9692 (pm20) cc_final: 0.9386 (tt0) REVERT: P 171 MET cc_start: 0.9651 (mmp) cc_final: 0.9450 (mmm) REVERT: P 183 MET cc_start: 0.7892 (mmm) cc_final: 0.7658 (mmm) REVERT: Q 1 MET cc_start: 0.5495 (ttt) cc_final: 0.5226 (tmm) REVERT: Q 44 LEU cc_start: 0.9625 (tp) cc_final: 0.9337 (tp) REVERT: Q 69 MET cc_start: 0.9091 (mmm) cc_final: 0.8648 (tpt) REVERT: Q 118 MET cc_start: 0.8392 (tpt) cc_final: 0.8122 (tpp) REVERT: R 86 MET cc_start: 0.9630 (mtm) cc_final: 0.8922 (mtm) REVERT: R 100 MET cc_start: 0.9182 (mtt) cc_final: 0.8188 (tmm) REVERT: R 175 ASN cc_start: 0.8212 (m-40) cc_final: 0.7915 (m110) REVERT: S 83 MET cc_start: 0.7569 (ttt) cc_final: 0.7299 (tpt) REVERT: T 26 MET cc_start: 0.8720 (mmp) cc_final: 0.8042 (mmm) REVERT: T 51 LEU cc_start: 0.9716 (tp) cc_final: 0.9470 (tp) REVERT: T 96 MET cc_start: 0.9636 (mmm) cc_final: 0.8511 (tpt) REVERT: T 122 LEU cc_start: 0.8778 (tp) cc_final: 0.8546 (tp) REVERT: T 173 MET cc_start: 0.9711 (mmm) cc_final: 0.9303 (tpp) REVERT: T 214 MET cc_start: 0.9419 (mpp) cc_final: 0.9203 (mpp) REVERT: g 134 LEU cc_start: 0.9433 (mt) cc_final: 0.9176 (tp) REVERT: h 113 ARG cc_start: 0.9568 (mtt-85) cc_final: 0.9153 (mtm180) REVERT: i 25 MET cc_start: 0.9580 (mmp) cc_final: 0.9266 (mmp) REVERT: i 26 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9294 (mt-10) REVERT: i 34 CYS cc_start: 0.5814 (m) cc_final: 0.5569 (m) REVERT: i 71 ASP cc_start: 0.7724 (p0) cc_final: 0.7462 (m-30) REVERT: i 72 MET cc_start: 0.8603 (mpp) cc_final: 0.8275 (mpp) REVERT: j 106 TYR cc_start: 0.9662 (t80) cc_final: 0.9356 (t80) REVERT: j 133 ILE cc_start: 0.9384 (mp) cc_final: 0.8994 (tt) REVERT: k 78 MET cc_start: 0.9033 (ptp) cc_final: 0.8469 (ppp) REVERT: k 90 ASP cc_start: 0.9449 (t0) cc_final: 0.9206 (p0) REVERT: k 107 MET cc_start: 0.8357 (ttm) cc_final: 0.8002 (ttm) REVERT: k 112 VAL cc_start: 0.9733 (t) cc_final: 0.9261 (t) REVERT: k 143 PHE cc_start: 0.9379 (m-10) cc_final: 0.9119 (m-80) REVERT: k 156 MET cc_start: 0.9142 (ptm) cc_final: 0.8901 (tmm) REVERT: m 47 PHE cc_start: 0.9622 (m-10) cc_final: 0.9013 (m-10) REVERT: m 75 MET cc_start: 0.9560 (mpp) cc_final: 0.9266 (mpp) REVERT: m 150 MET cc_start: 0.9575 (tmm) cc_final: 0.9253 (ppp) REVERT: n 4 MET cc_start: 0.9695 (ttt) cc_final: 0.9273 (tmm) REVERT: n 14 LEU cc_start: 0.9578 (mp) cc_final: 0.9144 (tp) REVERT: n 90 TYR cc_start: 0.9660 (m-10) cc_final: 0.9435 (m-10) REVERT: o 64 GLU cc_start: 0.9880 (tp30) cc_final: 0.9656 (tp30) REVERT: o 82 MET cc_start: 0.9466 (mtt) cc_final: 0.9204 (mmm) REVERT: o 127 MET cc_start: 0.8246 (mmt) cc_final: 0.7492 (mtt) REVERT: o 146 MET cc_start: 0.8652 (mtt) cc_final: 0.8388 (mtt) REVERT: p 12 MET cc_start: 0.7847 (tpt) cc_final: 0.6579 (tpp) REVERT: p 14 MET cc_start: 0.9323 (ttm) cc_final: 0.8823 (mmm) REVERT: p 88 MET cc_start: 0.9493 (ptp) cc_final: 0.9221 (ptp) REVERT: p 149 MET cc_start: 0.8692 (mmp) cc_final: 0.8264 (mmp) REVERT: q 36 PHE cc_start: 0.8819 (m-10) cc_final: 0.8360 (m-80) REVERT: q 58 GLU cc_start: 0.9134 (tp30) cc_final: 0.8928 (tp30) REVERT: q 118 MET cc_start: 0.8128 (tpp) cc_final: 0.7807 (tpp) REVERT: q 167 LEU cc_start: 0.9793 (tt) cc_final: 0.9483 (mt) REVERT: r 32 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9140 (ttpt) REVERT: r 45 MET cc_start: 0.8827 (ttt) cc_final: 0.8590 (tpp) REVERT: r 82 LEU cc_start: 0.9895 (tt) cc_final: 0.9609 (tt) REVERT: r 86 MET cc_start: 0.9549 (mmp) cc_final: 0.9335 (mmp) REVERT: r 93 MET cc_start: 0.9465 (mtt) cc_final: 0.9134 (mtt) REVERT: r 100 MET cc_start: 0.9287 (mtt) cc_final: 0.8728 (tpp) REVERT: r 117 GLU cc_start: 0.9709 (mm-30) cc_final: 0.9455 (tm-30) REVERT: r 139 MET cc_start: 0.9614 (ttp) cc_final: 0.9176 (ptt) REVERT: s 130 TYR cc_start: 0.8977 (p90) cc_final: 0.8594 (p90) REVERT: s 144 MET cc_start: 0.9633 (mmp) cc_final: 0.9387 (mmm) REVERT: t 5 MET cc_start: 0.9217 (mmp) cc_final: 0.8997 (mmm) REVERT: t 12 LEU cc_start: 0.9877 (mt) cc_final: 0.9573 (pp) REVERT: t 26 MET cc_start: 0.8613 (mmp) cc_final: 0.7947 (mmm) REVERT: t 42 ILE cc_start: 0.8315 (mt) cc_final: 0.7503 (mt) REVERT: t 43 MET cc_start: 0.9228 (tmm) cc_final: 0.8628 (tmm) REVERT: t 60 PHE cc_start: 0.9252 (t80) cc_final: 0.8187 (m-80) REVERT: t 62 TYR cc_start: 0.9823 (t80) cc_final: 0.9597 (t80) REVERT: t 70 MET cc_start: 0.9774 (mtm) cc_final: 0.9488 (mtm) REVERT: t 96 MET cc_start: 0.9729 (mmm) cc_final: 0.8976 (tpt) REVERT: t 173 MET cc_start: 0.9473 (mtp) cc_final: 0.9156 (mtt) outliers start: 13 outliers final: 3 residues processed: 840 average time/residue: 0.9306 time to fit residues: 1342.2359 Evaluate side-chains 684 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 680 time to evaluate : 8.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1157 optimal weight: 2.9990 chunk 880 optimal weight: 6.9990 chunk 608 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 chunk 559 optimal weight: 10.0000 chunk 786 optimal weight: 30.0000 chunk 1175 optimal weight: 10.0000 chunk 1244 optimal weight: 7.9990 chunk 614 optimal weight: 30.0000 chunk 1114 optimal weight: 9.9990 chunk 335 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN c 221 HIS c 254 ASN ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN U 139 GLN U 421 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 ASN V 199 ASN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 GLN W 264 GLN ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 363 ASN Z 193 ASN Z 243 GLN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN B 207 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN J 122 ASN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 GLN M 101 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 GLN ** T 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 HIS m 101 ASN ** m 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 173 ASN q 82 ASN r 38 ASN r 162 GLN t 188 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 103051 Z= 0.241 Angle : 0.713 14.733 139379 Z= 0.371 Chirality : 0.045 0.286 15874 Planarity : 0.005 0.125 18022 Dihedral : 7.029 83.927 14347 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.05 % Favored : 90.82 % Rotamer: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.07), residues: 12934 helix: -0.36 (0.06), residues: 6006 sheet: -1.42 (0.11), residues: 1792 loop : -2.44 (0.08), residues: 5136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP W 80 HIS 0.013 0.001 HIS W 361 PHE 0.039 0.002 PHE U 88 TYR 0.028 0.002 TYR j 21 ARG 0.021 0.001 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 751 time to evaluate : 9.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3665 (mtp) cc_final: 0.2751 (ptt) REVERT: a 280 MET cc_start: 0.8630 (ptp) cc_final: 0.8416 (ptp) REVERT: b 7 MET cc_start: 0.6142 (tpp) cc_final: 0.5859 (tpp) REVERT: c 95 MET cc_start: 0.9783 (tpp) cc_final: 0.9273 (mmm) REVERT: c 97 ASP cc_start: 0.9639 (t70) cc_final: 0.9432 (p0) REVERT: c 167 MET cc_start: 0.8922 (mtp) cc_final: 0.8280 (tmm) REVERT: c 168 MET cc_start: 0.7827 (tmm) cc_final: 0.7535 (tmm) REVERT: c 226 MET cc_start: 0.7557 (tpt) cc_final: 0.7325 (tpt) REVERT: d 75 MET cc_start: 0.8568 (tpt) cc_final: 0.8354 (tpt) REVERT: d 116 HIS cc_start: 0.9114 (m90) cc_final: 0.8754 (m170) REVERT: e 67 MET cc_start: 0.4298 (mtt) cc_final: 0.3717 (mtt) REVERT: f 133 MET cc_start: 0.6166 (mtt) cc_final: 0.5848 (mtt) REVERT: f 340 MET cc_start: 0.6242 (ptt) cc_final: 0.5085 (pmm) REVERT: f 670 MET cc_start: 0.8833 (mmp) cc_final: 0.8604 (mmm) REVERT: U 325 MET cc_start: 0.8404 (ptm) cc_final: 0.8075 (mmp) REVERT: U 333 MET cc_start: 0.9495 (ppp) cc_final: 0.9279 (ppp) REVERT: U 423 MET cc_start: 0.9276 (mpp) cc_final: 0.8327 (ppp) REVERT: U 675 MET cc_start: 0.9742 (mmm) cc_final: 0.9429 (tpp) REVERT: U 766 PHE cc_start: 0.9635 (t80) cc_final: 0.9411 (t80) REVERT: U 894 MET cc_start: 0.8196 (ttt) cc_final: 0.7588 (tmm) REVERT: V 37 MET cc_start: 0.8809 (mmm) cc_final: 0.8276 (mmm) REVERT: V 409 MET cc_start: 0.9245 (ptp) cc_final: 0.8908 (ppp) REVERT: W 16 MET cc_start: 0.8801 (mmt) cc_final: 0.7964 (mmt) REVERT: W 177 MET cc_start: 0.7936 (tpt) cc_final: 0.7258 (mmm) REVERT: Y 73 MET cc_start: 0.8324 (mtp) cc_final: 0.7863 (ttt) REVERT: Y 104 MET cc_start: 0.9573 (tpp) cc_final: 0.9302 (tpp) REVERT: Y 152 MET cc_start: 0.6514 (mmp) cc_final: 0.5409 (mpp) REVERT: Y 282 MET cc_start: 0.7970 (mmt) cc_final: 0.7536 (mmt) REVERT: Y 302 HIS cc_start: 0.9194 (t70) cc_final: 0.8762 (t70) REVERT: Z 78 MET cc_start: 0.9220 (tpp) cc_final: 0.8731 (tpp) REVERT: A 156 LYS cc_start: 0.9441 (tttt) cc_final: 0.9056 (tptp) REVERT: A 164 MET cc_start: 0.8469 (mpp) cc_final: 0.7563 (mpp) REVERT: A 256 MET cc_start: 0.9412 (mmp) cc_final: 0.9035 (mmm) REVERT: A 263 MET cc_start: 0.9438 (tpt) cc_final: 0.9099 (tpp) REVERT: A 299 MET cc_start: 0.8992 (ptp) cc_final: 0.8685 (ptp) REVERT: B 271 PHE cc_start: 0.9431 (m-80) cc_final: 0.9213 (m-80) REVERT: B 405 MET cc_start: 0.9589 (mmm) cc_final: 0.8936 (mtp) REVERT: B 428 TYR cc_start: 0.9685 (m-80) cc_final: 0.9297 (m-80) REVERT: C 124 HIS cc_start: 0.8985 (t70) cc_final: 0.8491 (t-90) REVERT: C 351 MET cc_start: 0.7631 (mtt) cc_final: 0.6742 (ttm) REVERT: D 111 TYR cc_start: 0.8974 (m-80) cc_final: 0.8592 (m-80) REVERT: D 214 MET cc_start: 0.9287 (ptp) cc_final: 0.8874 (ptp) REVERT: D 296 MET cc_start: 0.8626 (tpt) cc_final: 0.8308 (tpt) REVERT: D 352 MET cc_start: 0.6212 (mpp) cc_final: 0.5840 (mpp) REVERT: E 102 MET cc_start: 0.9589 (pmm) cc_final: 0.9205 (mpp) REVERT: E 352 MET cc_start: 0.9502 (tmm) cc_final: 0.8964 (tmm) REVERT: E 372 ARG cc_start: 0.9717 (mtt90) cc_final: 0.9316 (tmm160) REVERT: F 225 MET cc_start: 0.6390 (ttp) cc_final: 0.6127 (ttm) REVERT: G 19 GLU cc_start: 0.9653 (pm20) cc_final: 0.9441 (mp0) REVERT: G 83 MET cc_start: 0.9649 (mmp) cc_final: 0.9388 (mmm) REVERT: G 125 TYR cc_start: 0.9741 (m-80) cc_final: 0.9521 (m-80) REVERT: G 138 MET cc_start: 0.9357 (ttm) cc_final: 0.9007 (tpp) REVERT: H 121 TYR cc_start: 0.9651 (m-80) cc_final: 0.9380 (m-80) REVERT: I 45 LEU cc_start: 0.9904 (mt) cc_final: 0.9637 (tt) REVERT: I 72 MET cc_start: 0.8412 (ptp) cc_final: 0.8026 (mtm) REVERT: K 143 PHE cc_start: 0.8854 (m-80) cc_final: 0.8273 (m-80) REVERT: K 156 MET cc_start: 0.8957 (tmm) cc_final: 0.8687 (tmm) REVERT: K 228 MET cc_start: 0.8256 (pmm) cc_final: 0.8004 (pmm) REVERT: L 41 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9321 (mmmt) REVERT: L 108 LEU cc_start: 0.9779 (tt) cc_final: 0.9507 (mp) REVERT: L 153 TYR cc_start: 0.9103 (p90) cc_final: 0.8593 (p90) REVERT: L 176 MET cc_start: 0.9264 (ptp) cc_final: 0.8857 (ptp) REVERT: M 27 MET cc_start: 0.9011 (mtt) cc_final: 0.8611 (mmt) REVERT: M 67 PHE cc_start: 0.7967 (m-10) cc_final: 0.7608 (m-10) REVERT: M 75 MET cc_start: 0.9435 (mtp) cc_final: 0.8877 (mmt) REVERT: M 135 PHE cc_start: 0.9556 (p90) cc_final: 0.9211 (p90) REVERT: M 181 MET cc_start: 0.6638 (ptm) cc_final: 0.6313 (ptm) REVERT: M 184 MET cc_start: 0.8438 (ttp) cc_final: 0.8199 (tmm) REVERT: N 51 ASP cc_start: 0.9563 (m-30) cc_final: 0.9126 (t0) REVERT: N 119 MET cc_start: 0.9177 (mmt) cc_final: 0.8884 (mmp) REVERT: P 14 MET cc_start: 0.9486 (ttm) cc_final: 0.8886 (ttm) REVERT: P 96 TYR cc_start: 0.9776 (t80) cc_final: 0.9524 (t80) REVERT: P 117 PHE cc_start: 0.9227 (p90) cc_final: 0.8962 (p90) REVERT: P 171 MET cc_start: 0.9728 (mmp) cc_final: 0.9515 (mmm) REVERT: Q 1 MET cc_start: 0.5434 (ttt) cc_final: 0.4703 (tmm) REVERT: Q 44 LEU cc_start: 0.9677 (tp) cc_final: 0.9353 (tp) REVERT: Q 69 MET cc_start: 0.9049 (mmm) cc_final: 0.8609 (tpt) REVERT: Q 118 MET cc_start: 0.8546 (tpt) cc_final: 0.8090 (tpp) REVERT: R 86 MET cc_start: 0.9493 (mtm) cc_final: 0.8883 (mtm) REVERT: R 100 MET cc_start: 0.8927 (mtt) cc_final: 0.7801 (tpp) REVERT: R 175 ASN cc_start: 0.8285 (m-40) cc_final: 0.8000 (m110) REVERT: T 26 MET cc_start: 0.8771 (mmp) cc_final: 0.8157 (mmm) REVERT: T 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9472 (tp) REVERT: T 96 MET cc_start: 0.9623 (mmm) cc_final: 0.8539 (tpt) REVERT: T 127 MET cc_start: 0.7905 (ttp) cc_final: 0.6635 (ttm) REVERT: T 173 MET cc_start: 0.9721 (mmm) cc_final: 0.9394 (tpp) REVERT: T 214 MET cc_start: 0.9439 (mpp) cc_final: 0.9177 (mpp) REVERT: g 134 LEU cc_start: 0.9473 (mt) cc_final: 0.9253 (tp) REVERT: h 113 ARG cc_start: 0.9556 (mtt-85) cc_final: 0.9109 (mtm180) REVERT: i 25 MET cc_start: 0.9629 (mmp) cc_final: 0.9350 (mmm) REVERT: i 26 GLU cc_start: 0.9517 (mm-30) cc_final: 0.9305 (mt-10) REVERT: i 34 CYS cc_start: 0.6458 (m) cc_final: 0.6226 (m) REVERT: i 71 ASP cc_start: 0.7932 (p0) cc_final: 0.7606 (m-30) REVERT: i 72 MET cc_start: 0.8711 (mpp) cc_final: 0.8431 (mpp) REVERT: i 174 MET cc_start: 0.9418 (ttm) cc_final: 0.9120 (mtp) REVERT: j 70 CYS cc_start: 0.9524 (m) cc_final: 0.9099 (m) REVERT: j 96 LEU cc_start: 0.9429 (tt) cc_final: 0.9148 (tt) REVERT: j 106 TYR cc_start: 0.9672 (t80) cc_final: 0.9242 (t80) REVERT: j 133 ILE cc_start: 0.9452 (mp) cc_final: 0.9176 (tp) REVERT: k 78 MET cc_start: 0.8987 (ptp) cc_final: 0.8451 (ppp) REVERT: k 90 ASP cc_start: 0.9491 (t0) cc_final: 0.9203 (p0) REVERT: k 107 MET cc_start: 0.8260 (ttm) cc_final: 0.7875 (ttm) REVERT: l 115 LYS cc_start: 0.9569 (tptp) cc_final: 0.9186 (mmmm) REVERT: m 47 PHE cc_start: 0.9630 (m-10) cc_final: 0.8662 (m-10) REVERT: m 75 MET cc_start: 0.9566 (mpp) cc_final: 0.9242 (mpp) REVERT: m 150 MET cc_start: 0.9625 (tmm) cc_final: 0.9285 (ppp) REVERT: m 184 MET cc_start: 0.9004 (ppp) cc_final: 0.8400 (ppp) REVERT: n 4 MET cc_start: 0.9721 (ttt) cc_final: 0.9300 (tmm) REVERT: n 14 LEU cc_start: 0.9619 (mp) cc_final: 0.9196 (tp) REVERT: o 64 GLU cc_start: 0.9880 (tp30) cc_final: 0.9654 (tp30) REVERT: o 82 MET cc_start: 0.9461 (mtt) cc_final: 0.9216 (mmm) REVERT: o 93 TYR cc_start: 0.8895 (m-80) cc_final: 0.8609 (m-80) REVERT: o 146 MET cc_start: 0.8808 (mtt) cc_final: 0.8571 (mtt) REVERT: p 146 MET cc_start: 0.9696 (mpp) cc_final: 0.9331 (ptt) REVERT: p 149 MET cc_start: 0.8955 (mmp) cc_final: 0.8734 (mmp) REVERT: p 171 MET cc_start: 0.9800 (mmp) cc_final: 0.9321 (mmm) REVERT: q 1 MET cc_start: 0.5180 (ttt) cc_final: 0.4643 (tmm) REVERT: q 36 PHE cc_start: 0.8884 (m-10) cc_final: 0.8448 (m-80) REVERT: q 58 GLU cc_start: 0.8903 (tp30) cc_final: 0.8627 (tp30) REVERT: q 118 MET cc_start: 0.8203 (tpp) cc_final: 0.7847 (tpp) REVERT: q 167 LEU cc_start: 0.9861 (tt) cc_final: 0.9577 (mt) REVERT: r 82 LEU cc_start: 0.9927 (tt) cc_final: 0.9671 (tt) REVERT: r 100 MET cc_start: 0.9236 (mtt) cc_final: 0.8682 (tpp) REVERT: r 117 GLU cc_start: 0.9760 (mm-30) cc_final: 0.9477 (tm-30) REVERT: r 139 MET cc_start: 0.9587 (ttp) cc_final: 0.9112 (ptm) REVERT: s 130 TYR cc_start: 0.8996 (p90) cc_final: 0.8642 (p90) REVERT: t 26 MET cc_start: 0.8708 (mmp) cc_final: 0.8032 (mmm) REVERT: t 42 ILE cc_start: 0.8709 (mt) cc_final: 0.8452 (mp) REVERT: t 43 MET cc_start: 0.9195 (tmm) cc_final: 0.8897 (tmm) REVERT: t 60 PHE cc_start: 0.9272 (t80) cc_final: 0.8298 (m-80) REVERT: t 62 TYR cc_start: 0.9813 (t80) cc_final: 0.9567 (t80) REVERT: t 96 MET cc_start: 0.9718 (mmm) cc_final: 0.8948 (tpt) REVERT: t 127 MET cc_start: 0.7372 (ttp) cc_final: 0.6365 (ttp) outliers start: 8 outliers final: 3 residues processed: 759 average time/residue: 0.9233 time to fit residues: 1218.9434 Evaluate side-chains 630 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 627 time to evaluate : 8.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1036 optimal weight: 8.9990 chunk 706 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 926 optimal weight: 9.9990 chunk 513 optimal weight: 0.3980 chunk 1062 optimal weight: 3.9990 chunk 860 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 635 optimal weight: 2.9990 chunk 1117 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 6 GLN e 42 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN f 387 GLN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 540 GLN U 18 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 218 HIS ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 270 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 157 GLN T 188 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN q 87 ASN s 79 ASN t 188 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 103051 Z= 0.205 Angle : 0.681 13.818 139379 Z= 0.354 Chirality : 0.044 0.344 15874 Planarity : 0.005 0.118 18022 Dihedral : 6.836 89.607 14347 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.84 % Favored : 91.06 % Rotamer: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.07), residues: 12934 helix: -0.09 (0.07), residues: 6012 sheet: -1.28 (0.12), residues: 1791 loop : -2.32 (0.09), residues: 5131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP W 80 HIS 0.019 0.001 HIS Z 196 PHE 0.032 0.002 PHE f 304 TYR 0.025 0.002 TYR U 650 ARG 0.024 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 740 time to evaluate : 8.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3646 (mtp) cc_final: 0.2653 (ptt) REVERT: b 7 MET cc_start: 0.6159 (tpp) cc_final: 0.5888 (tpp) REVERT: c 95 MET cc_start: 0.9796 (tpp) cc_final: 0.9342 (mmm) REVERT: c 97 ASP cc_start: 0.9658 (t70) cc_final: 0.9408 (p0) REVERT: c 167 MET cc_start: 0.8918 (mtp) cc_final: 0.8303 (tmm) REVERT: d 112 VAL cc_start: 0.8695 (t) cc_final: 0.8302 (t) REVERT: d 116 HIS cc_start: 0.9079 (m90) cc_final: 0.8684 (m170) REVERT: e 67 MET cc_start: 0.4067 (mtt) cc_final: 0.3561 (mtt) REVERT: f 133 MET cc_start: 0.6079 (mtt) cc_final: 0.5755 (mtt) REVERT: f 209 MET cc_start: 0.7237 (ppp) cc_final: 0.4834 (mmt) REVERT: f 340 MET cc_start: 0.6217 (ptt) cc_final: 0.5467 (pmm) REVERT: f 469 TYR cc_start: 0.8990 (t80) cc_final: 0.8762 (t80) REVERT: f 670 MET cc_start: 0.8821 (mmp) cc_final: 0.8617 (mmm) REVERT: U 188 MET cc_start: 0.5251 (ttm) cc_final: 0.4972 (ttm) REVERT: U 325 MET cc_start: 0.8414 (ptm) cc_final: 0.8074 (mmp) REVERT: U 560 MET cc_start: 0.8991 (mmt) cc_final: 0.8734 (mmt) REVERT: U 675 MET cc_start: 0.9725 (mmm) cc_final: 0.9418 (tpp) REVERT: U 766 PHE cc_start: 0.9662 (t80) cc_final: 0.9429 (t80) REVERT: U 894 MET cc_start: 0.8121 (ttt) cc_final: 0.7547 (tmm) REVERT: V 37 MET cc_start: 0.8843 (mmm) cc_final: 0.8287 (mmm) REVERT: V 409 MET cc_start: 0.9222 (ptp) cc_final: 0.8838 (ppp) REVERT: V 463 MET cc_start: 0.8542 (mmp) cc_final: 0.8298 (mmm) REVERT: W 16 MET cc_start: 0.8805 (mmt) cc_final: 0.7919 (mmt) REVERT: W 88 MET cc_start: 0.6473 (mtp) cc_final: 0.6157 (mtm) REVERT: W 315 MET cc_start: 0.7407 (mtt) cc_final: 0.7201 (mtt) REVERT: Y 73 MET cc_start: 0.8320 (mtp) cc_final: 0.7899 (ttm) REVERT: Y 104 MET cc_start: 0.9595 (tpp) cc_final: 0.9329 (tpp) REVERT: Y 152 MET cc_start: 0.6526 (mmp) cc_final: 0.5461 (mpp) REVERT: Y 302 HIS cc_start: 0.9198 (t70) cc_final: 0.8777 (t70) REVERT: Z 78 MET cc_start: 0.9140 (tpp) cc_final: 0.8663 (tpp) REVERT: A 156 LYS cc_start: 0.9461 (tttt) cc_final: 0.9139 (tmtt) REVERT: A 164 MET cc_start: 0.8113 (mpp) cc_final: 0.7871 (mpp) REVERT: A 263 MET cc_start: 0.9428 (tpt) cc_final: 0.9082 (tpp) REVERT: A 299 MET cc_start: 0.8745 (ptp) cc_final: 0.8432 (ptp) REVERT: B 271 PHE cc_start: 0.9411 (m-80) cc_final: 0.9185 (m-80) REVERT: B 329 MET cc_start: 0.8258 (ppp) cc_final: 0.7915 (ppp) REVERT: B 405 MET cc_start: 0.9577 (mmm) cc_final: 0.8923 (mtp) REVERT: B 428 TYR cc_start: 0.9667 (m-80) cc_final: 0.9284 (m-80) REVERT: C 124 HIS cc_start: 0.9005 (t70) cc_final: 0.8608 (t70) REVERT: C 230 MET cc_start: 0.8598 (ptm) cc_final: 0.8294 (ptt) REVERT: C 351 MET cc_start: 0.7444 (ttm) cc_final: 0.7162 (ttm) REVERT: D 214 MET cc_start: 0.9300 (ptp) cc_final: 0.8896 (ptp) REVERT: D 235 PHE cc_start: 0.8660 (m-10) cc_final: 0.8340 (m-80) REVERT: D 296 MET cc_start: 0.8625 (tpt) cc_final: 0.8286 (tpt) REVERT: D 352 MET cc_start: 0.6090 (mpp) cc_final: 0.5726 (mpp) REVERT: E 102 MET cc_start: 0.9581 (pmm) cc_final: 0.9223 (mpp) REVERT: E 352 MET cc_start: 0.9516 (tmm) cc_final: 0.8976 (tmm) REVERT: E 372 ARG cc_start: 0.9724 (mtt90) cc_final: 0.9296 (tmm160) REVERT: F 225 MET cc_start: 0.6299 (ttp) cc_final: 0.6069 (ttm) REVERT: F 373 MET cc_start: 0.6717 (mmm) cc_final: 0.6374 (tpp) REVERT: F 421 MET cc_start: 0.9649 (mmp) cc_final: 0.9391 (mmm) REVERT: G 19 GLU cc_start: 0.9621 (pm20) cc_final: 0.9388 (mp0) REVERT: G 83 MET cc_start: 0.9622 (mmp) cc_final: 0.9346 (mmm) REVERT: G 103 TYR cc_start: 0.9586 (t80) cc_final: 0.9172 (t80) REVERT: G 125 TYR cc_start: 0.9714 (m-80) cc_final: 0.9472 (m-80) REVERT: G 138 MET cc_start: 0.9376 (ttm) cc_final: 0.9060 (ttp) REVERT: H 121 TYR cc_start: 0.9679 (m-80) cc_final: 0.9454 (m-80) REVERT: I 45 LEU cc_start: 0.9909 (mt) cc_final: 0.9638 (tt) REVERT: J 38 ARG cc_start: 0.9527 (ttt180) cc_final: 0.9126 (mmp-170) REVERT: K 59 MET cc_start: 0.8629 (ttt) cc_final: 0.8136 (ttt) REVERT: K 143 PHE cc_start: 0.8846 (m-80) cc_final: 0.8196 (m-80) REVERT: K 156 MET cc_start: 0.8958 (tmm) cc_final: 0.8692 (tmm) REVERT: K 206 MET cc_start: 0.7857 (ptp) cc_final: 0.7643 (ptt) REVERT: K 228 MET cc_start: 0.8199 (pmm) cc_final: 0.7929 (pmm) REVERT: L 41 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9341 (mmmt) REVERT: L 108 LEU cc_start: 0.9787 (tt) cc_final: 0.9507 (mp) REVERT: L 153 TYR cc_start: 0.9042 (p90) cc_final: 0.8584 (p90) REVERT: M 27 MET cc_start: 0.9044 (mtt) cc_final: 0.8611 (mmm) REVERT: M 67 PHE cc_start: 0.7960 (m-10) cc_final: 0.7568 (m-10) REVERT: M 75 MET cc_start: 0.9415 (mtp) cc_final: 0.8894 (mmt) REVERT: M 135 PHE cc_start: 0.9538 (p90) cc_final: 0.9233 (p90) REVERT: M 136 MET cc_start: 0.9254 (mmp) cc_final: 0.8920 (mtt) REVERT: M 181 MET cc_start: 0.6562 (ptm) cc_final: 0.6283 (ptm) REVERT: M 184 MET cc_start: 0.8379 (ttp) cc_final: 0.8004 (ttm) REVERT: N 51 ASP cc_start: 0.9579 (m-30) cc_final: 0.9193 (t0) REVERT: N 119 MET cc_start: 0.9281 (mmt) cc_final: 0.9003 (mmp) REVERT: P 14 MET cc_start: 0.9526 (ttm) cc_final: 0.8927 (ttm) REVERT: P 96 TYR cc_start: 0.9744 (t80) cc_final: 0.9437 (t80) REVERT: P 117 PHE cc_start: 0.9227 (p90) cc_final: 0.8966 (p90) REVERT: P 149 MET cc_start: 0.9565 (tpp) cc_final: 0.9354 (tpt) REVERT: Q 1 MET cc_start: 0.5437 (ttt) cc_final: 0.4704 (tmm) REVERT: Q 44 LEU cc_start: 0.9708 (tp) cc_final: 0.9375 (tp) REVERT: Q 69 MET cc_start: 0.9069 (mmm) cc_final: 0.8746 (mmm) REVERT: Q 118 MET cc_start: 0.8948 (tpt) cc_final: 0.8419 (tpp) REVERT: R 100 MET cc_start: 0.8532 (mtt) cc_final: 0.7785 (tpp) REVERT: S 74 MET cc_start: 0.9644 (ptp) cc_final: 0.9428 (ptp) REVERT: S 145 LEU cc_start: 0.9900 (mm) cc_final: 0.9538 (tp) REVERT: S 149 LEU cc_start: 0.9659 (mt) cc_final: 0.9340 (mt) REVERT: T 26 MET cc_start: 0.8885 (mmp) cc_final: 0.8084 (mmm) REVERT: T 51 LEU cc_start: 0.9699 (tp) cc_final: 0.9484 (tp) REVERT: T 96 MET cc_start: 0.9619 (mmm) cc_final: 0.8498 (tpt) REVERT: T 127 MET cc_start: 0.7952 (ttp) cc_final: 0.6753 (ttm) REVERT: T 173 MET cc_start: 0.9723 (mmm) cc_final: 0.9369 (tpp) REVERT: T 214 MET cc_start: 0.9449 (mpp) cc_final: 0.9164 (mpp) REVERT: g 134 LEU cc_start: 0.9389 (mt) cc_final: 0.9020 (tp) REVERT: i 25 MET cc_start: 0.9630 (mmp) cc_final: 0.9345 (mmm) REVERT: i 26 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9319 (mt-10) REVERT: i 90 LEU cc_start: 0.9697 (mt) cc_final: 0.9397 (mt) REVERT: i 174 MET cc_start: 0.9423 (ttm) cc_final: 0.9072 (mtp) REVERT: j 106 TYR cc_start: 0.9658 (t80) cc_final: 0.9213 (t80) REVERT: j 133 ILE cc_start: 0.9445 (mp) cc_final: 0.9132 (tp) REVERT: k 78 MET cc_start: 0.8957 (ptp) cc_final: 0.8438 (ppp) REVERT: k 90 ASP cc_start: 0.9499 (t0) cc_final: 0.9217 (p0) REVERT: k 107 MET cc_start: 0.8317 (ttm) cc_final: 0.8073 (ttp) REVERT: k 112 VAL cc_start: 0.9678 (t) cc_final: 0.9379 (t) REVERT: k 143 PHE cc_start: 0.9511 (m-10) cc_final: 0.9238 (m-10) REVERT: k 156 MET cc_start: 0.9577 (ppp) cc_final: 0.9329 (tmm) REVERT: l 115 LYS cc_start: 0.9605 (tptp) cc_final: 0.9212 (mmmm) REVERT: m 47 PHE cc_start: 0.9574 (m-10) cc_final: 0.8686 (m-10) REVERT: m 75 MET cc_start: 0.9530 (mpp) cc_final: 0.9206 (mpp) REVERT: m 150 MET cc_start: 0.9642 (tmm) cc_final: 0.9315 (ppp) REVERT: m 184 MET cc_start: 0.9013 (ppp) cc_final: 0.8391 (ppp) REVERT: m 188 ASP cc_start: 0.9830 (m-30) cc_final: 0.9620 (m-30) REVERT: n 4 MET cc_start: 0.9716 (ttt) cc_final: 0.9358 (tmm) REVERT: n 14 LEU cc_start: 0.9599 (mp) cc_final: 0.9296 (tp) REVERT: n 90 TYR cc_start: 0.9817 (m-80) cc_final: 0.9597 (m-10) REVERT: n 116 MET cc_start: 0.9584 (mtp) cc_final: 0.9379 (tpp) REVERT: n 119 MET cc_start: 0.9622 (tpp) cc_final: 0.9415 (tpp) REVERT: o 64 GLU cc_start: 0.9868 (tp30) cc_final: 0.9647 (tp30) REVERT: o 82 MET cc_start: 0.9455 (mtt) cc_final: 0.9220 (mmm) REVERT: o 93 TYR cc_start: 0.8847 (m-80) cc_final: 0.8569 (m-80) REVERT: o 146 MET cc_start: 0.8786 (mtt) cc_final: 0.8558 (mtt) REVERT: p 14 MET cc_start: 0.9014 (ttt) cc_final: 0.8698 (tpp) REVERT: p 51 ILE cc_start: 0.9350 (tt) cc_final: 0.9144 (tt) REVERT: p 146 MET cc_start: 0.9710 (mpp) cc_final: 0.9318 (ptt) REVERT: p 149 MET cc_start: 0.8955 (mmp) cc_final: 0.8733 (mmm) REVERT: p 171 MET cc_start: 0.9741 (mmp) cc_final: 0.9309 (mmm) REVERT: q 1 MET cc_start: 0.5349 (ttt) cc_final: 0.4799 (tmm) REVERT: q 36 PHE cc_start: 0.8853 (m-10) cc_final: 0.8424 (m-80) REVERT: q 118 MET cc_start: 0.8412 (tpp) cc_final: 0.7971 (tpp) REVERT: q 167 LEU cc_start: 0.9876 (tt) cc_final: 0.9590 (mt) REVERT: r 82 LEU cc_start: 0.9931 (tt) cc_final: 0.9633 (tt) REVERT: r 86 MET cc_start: 0.9528 (mmp) cc_final: 0.9308 (mmp) REVERT: r 100 MET cc_start: 0.9192 (mtt) cc_final: 0.8620 (tpp) REVERT: r 139 MET cc_start: 0.9583 (ttp) cc_final: 0.9092 (ptm) REVERT: t 5 MET cc_start: 0.9297 (mmp) cc_final: 0.8994 (mmm) REVERT: t 26 MET cc_start: 0.8783 (mmp) cc_final: 0.8156 (mmm) REVERT: t 42 ILE cc_start: 0.8659 (mt) cc_final: 0.8311 (mp) REVERT: t 43 MET cc_start: 0.9278 (tmm) cc_final: 0.8739 (tmm) REVERT: t 60 PHE cc_start: 0.9248 (t80) cc_final: 0.8343 (m-80) REVERT: t 62 TYR cc_start: 0.9802 (t80) cc_final: 0.9585 (t80) REVERT: t 96 MET cc_start: 0.9689 (mmm) cc_final: 0.8871 (tpt) REVERT: t 127 MET cc_start: 0.7444 (ttp) cc_final: 0.6469 (ttp) outliers start: 4 outliers final: 3 residues processed: 744 average time/residue: 0.8939 time to fit residues: 1157.8450 Evaluate side-chains 628 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 625 time to evaluate : 8.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 418 optimal weight: 10.0000 chunk 1121 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 730 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 1246 optimal weight: 0.9990 chunk 1034 optimal weight: 50.0000 chunk 576 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 412 optimal weight: 5.9990 chunk 654 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 464 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 12 HIS ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 314 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 84 ASN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 188 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 103051 Z= 0.197 Angle : 0.673 14.199 139379 Z= 0.347 Chirality : 0.044 0.292 15874 Planarity : 0.005 0.127 18022 Dihedral : 6.698 85.067 14347 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.76 % Favored : 91.14 % Rotamer: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.07), residues: 12934 helix: 0.08 (0.07), residues: 6042 sheet: -1.17 (0.12), residues: 1779 loop : -2.27 (0.09), residues: 5113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP W 80 HIS 0.012 0.001 HIS f 301 PHE 0.032 0.002 PHE f 304 TYR 0.024 0.002 TYR S 75 ARG 0.015 0.001 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 724 time to evaluate : 8.984 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3632 (mtp) cc_final: 0.2649 (ptt) REVERT: b 7 MET cc_start: 0.6161 (tpp) cc_final: 0.5883 (tpp) REVERT: c 95 MET cc_start: 0.9793 (tpp) cc_final: 0.9325 (mmm) REVERT: c 97 ASP cc_start: 0.9658 (t70) cc_final: 0.9398 (p0) REVERT: c 167 MET cc_start: 0.8900 (mtp) cc_final: 0.8308 (tmm) REVERT: d 75 MET cc_start: 0.8569 (tpt) cc_final: 0.8197 (tpt) REVERT: d 116 HIS cc_start: 0.9092 (m90) cc_final: 0.8698 (m170) REVERT: e 67 MET cc_start: 0.3755 (mtt) cc_final: 0.3235 (mtt) REVERT: f 209 MET cc_start: 0.7225 (ppp) cc_final: 0.4664 (mmp) REVERT: f 340 MET cc_start: 0.6210 (ptt) cc_final: 0.5504 (pmm) REVERT: f 469 TYR cc_start: 0.9014 (t80) cc_final: 0.8755 (t80) REVERT: f 670 MET cc_start: 0.8845 (mmp) cc_final: 0.8633 (mmm) REVERT: U 325 MET cc_start: 0.8501 (ptm) cc_final: 0.8236 (mmp) REVERT: U 333 MET cc_start: 0.9477 (ppp) cc_final: 0.9196 (ppp) REVERT: U 423 MET cc_start: 0.9293 (mpp) cc_final: 0.8336 (ppp) REVERT: U 560 MET cc_start: 0.9013 (mmt) cc_final: 0.8697 (mmt) REVERT: U 675 MET cc_start: 0.9726 (mmm) cc_final: 0.9414 (tpp) REVERT: U 766 PHE cc_start: 0.9674 (t80) cc_final: 0.9444 (t80) REVERT: U 894 MET cc_start: 0.8087 (ttt) cc_final: 0.7767 (tmm) REVERT: V 37 MET cc_start: 0.9040 (mmm) cc_final: 0.8487 (mmm) REVERT: V 409 MET cc_start: 0.9209 (ptp) cc_final: 0.8850 (ppp) REVERT: W 16 MET cc_start: 0.8777 (mmt) cc_final: 0.7817 (mmt) REVERT: W 88 MET cc_start: 0.6567 (mtp) cc_final: 0.6303 (mtm) REVERT: W 451 MET cc_start: 0.8758 (mmp) cc_final: 0.8510 (mmp) REVERT: Y 73 MET cc_start: 0.8298 (mtp) cc_final: 0.7824 (ttm) REVERT: Y 104 MET cc_start: 0.9602 (tpp) cc_final: 0.9377 (tpp) REVERT: Y 152 MET cc_start: 0.6304 (mmp) cc_final: 0.5217 (mpp) REVERT: Y 282 MET cc_start: 0.7698 (mmt) cc_final: 0.7265 (mmt) REVERT: Y 302 HIS cc_start: 0.9205 (t70) cc_final: 0.8744 (t70) REVERT: Z 78 MET cc_start: 0.9132 (tpp) cc_final: 0.8603 (tpp) REVERT: Z 267 ARG cc_start: 0.9514 (mpt180) cc_final: 0.9110 (mmt180) REVERT: A 156 LYS cc_start: 0.9432 (tttt) cc_final: 0.9092 (tmtt) REVERT: A 164 MET cc_start: 0.8038 (mpp) cc_final: 0.7797 (mpp) REVERT: A 256 MET cc_start: 0.9462 (mmp) cc_final: 0.9127 (mmm) REVERT: A 263 MET cc_start: 0.9413 (tpt) cc_final: 0.9062 (tpp) REVERT: A 299 MET cc_start: 0.8896 (ptp) cc_final: 0.8535 (ptp) REVERT: B 271 PHE cc_start: 0.9422 (m-80) cc_final: 0.9190 (m-80) REVERT: B 329 MET cc_start: 0.8323 (ppp) cc_final: 0.7935 (ppp) REVERT: B 405 MET cc_start: 0.9575 (mmm) cc_final: 0.8911 (mtp) REVERT: B 428 TYR cc_start: 0.9694 (m-80) cc_final: 0.9320 (m-80) REVERT: C 124 HIS cc_start: 0.8923 (t70) cc_final: 0.8493 (t70) REVERT: C 230 MET cc_start: 0.8572 (ptm) cc_final: 0.8348 (ptt) REVERT: C 351 MET cc_start: 0.7537 (ttm) cc_final: 0.7174 (ttm) REVERT: D 296 MET cc_start: 0.8680 (tpt) cc_final: 0.8332 (tpt) REVERT: D 352 MET cc_start: 0.6021 (mpp) cc_final: 0.5682 (mpp) REVERT: E 102 MET cc_start: 0.9573 (pmm) cc_final: 0.9229 (mpp) REVERT: E 352 MET cc_start: 0.9520 (tmm) cc_final: 0.9153 (tmm) REVERT: E 372 ARG cc_start: 0.9725 (mtt90) cc_final: 0.9286 (tmm160) REVERT: F 225 MET cc_start: 0.6329 (ttp) cc_final: 0.6126 (ttm) REVERT: F 373 MET cc_start: 0.6940 (mmm) cc_final: 0.6564 (tpp) REVERT: F 421 MET cc_start: 0.9665 (mmp) cc_final: 0.9434 (mmm) REVERT: G 19 GLU cc_start: 0.9648 (pm20) cc_final: 0.9418 (mp0) REVERT: G 83 MET cc_start: 0.9634 (mmp) cc_final: 0.9387 (mmm) REVERT: G 138 MET cc_start: 0.9500 (ttm) cc_final: 0.9156 (tpp) REVERT: H 121 TYR cc_start: 0.9704 (m-80) cc_final: 0.9500 (m-80) REVERT: I 45 LEU cc_start: 0.9910 (mt) cc_final: 0.9638 (tt) REVERT: J 38 ARG cc_start: 0.9527 (ttt180) cc_final: 0.9134 (mmp-170) REVERT: J 65 LEU cc_start: 0.9755 (mt) cc_final: 0.9542 (mt) REVERT: K 59 MET cc_start: 0.8659 (ttt) cc_final: 0.8164 (ttt) REVERT: K 143 PHE cc_start: 0.8757 (m-80) cc_final: 0.8229 (m-80) REVERT: K 156 MET cc_start: 0.8848 (tmm) cc_final: 0.8581 (tmm) REVERT: K 228 MET cc_start: 0.8020 (pmm) cc_final: 0.7572 (pmm) REVERT: L 108 LEU cc_start: 0.9787 (tt) cc_final: 0.9503 (mp) REVERT: L 153 TYR cc_start: 0.9058 (p90) cc_final: 0.8633 (p90) REVERT: L 176 MET cc_start: 0.9085 (ptp) cc_final: 0.8764 (ptp) REVERT: L 180 MET cc_start: 0.9364 (mmp) cc_final: 0.9092 (mmp) REVERT: M 27 MET cc_start: 0.9137 (mtt) cc_final: 0.8704 (mmm) REVERT: M 67 PHE cc_start: 0.7957 (m-10) cc_final: 0.7564 (m-10) REVERT: M 75 MET cc_start: 0.9388 (mtp) cc_final: 0.8883 (mmt) REVERT: M 135 PHE cc_start: 0.9575 (p90) cc_final: 0.9369 (p90) REVERT: M 184 MET cc_start: 0.8298 (ttp) cc_final: 0.7935 (ttm) REVERT: N 4 MET cc_start: 0.9010 (tpt) cc_final: 0.8804 (tpt) REVERT: N 51 ASP cc_start: 0.9582 (m-30) cc_final: 0.9197 (t0) REVERT: N 119 MET cc_start: 0.9379 (mmt) cc_final: 0.9178 (mmp) REVERT: O 54 MET cc_start: 0.9297 (mpp) cc_final: 0.9004 (mpp) REVERT: P 14 MET cc_start: 0.9520 (ttm) cc_final: 0.8900 (ttm) REVERT: P 96 TYR cc_start: 0.9716 (t80) cc_final: 0.9405 (t80) REVERT: P 117 PHE cc_start: 0.9231 (p90) cc_final: 0.8977 (p90) REVERT: Q 44 LEU cc_start: 0.9713 (tp) cc_final: 0.9383 (tp) REVERT: Q 69 MET cc_start: 0.9108 (mmm) cc_final: 0.8720 (mmm) REVERT: Q 118 MET cc_start: 0.8966 (tpt) cc_final: 0.8270 (tpp) REVERT: R 100 MET cc_start: 0.8302 (mtt) cc_final: 0.7828 (tpp) REVERT: T 26 MET cc_start: 0.8913 (mmp) cc_final: 0.8046 (mmm) REVERT: T 96 MET cc_start: 0.9599 (mmm) cc_final: 0.8476 (tpt) REVERT: T 127 MET cc_start: 0.7940 (ttp) cc_final: 0.6748 (ttm) REVERT: T 173 MET cc_start: 0.9720 (mmm) cc_final: 0.9369 (tpp) REVERT: T 214 MET cc_start: 0.9454 (mpp) cc_final: 0.9157 (mpp) REVERT: g 134 LEU cc_start: 0.9407 (mt) cc_final: 0.9051 (tp) REVERT: i 25 MET cc_start: 0.9622 (mmp) cc_final: 0.9328 (mmm) REVERT: i 26 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9316 (mt-10) REVERT: i 174 MET cc_start: 0.9395 (ttm) cc_final: 0.9011 (mtp) REVERT: j 71 MET cc_start: 0.8356 (tmm) cc_final: 0.7790 (ppp) REVERT: j 106 TYR cc_start: 0.9655 (t80) cc_final: 0.9199 (t80) REVERT: j 133 ILE cc_start: 0.9446 (mp) cc_final: 0.9145 (tp) REVERT: k 48 LEU cc_start: 0.9719 (tp) cc_final: 0.9462 (tp) REVERT: k 78 MET cc_start: 0.8930 (ptp) cc_final: 0.8433 (ppp) REVERT: k 90 ASP cc_start: 0.9532 (t0) cc_final: 0.9209 (p0) REVERT: k 112 VAL cc_start: 0.9643 (t) cc_final: 0.9300 (t) REVERT: k 143 PHE cc_start: 0.9468 (m-10) cc_final: 0.9171 (m-10) REVERT: k 156 MET cc_start: 0.9468 (ppp) cc_final: 0.8878 (tmm) REVERT: l 26 MET cc_start: 0.9468 (mmt) cc_final: 0.8915 (mmt) REVERT: l 86 ASN cc_start: 0.9818 (t0) cc_final: 0.9541 (m110) REVERT: l 115 LYS cc_start: 0.9616 (tptp) cc_final: 0.9223 (mmmm) REVERT: m 47 PHE cc_start: 0.9508 (m-10) cc_final: 0.8595 (m-10) REVERT: m 75 MET cc_start: 0.9523 (mpp) cc_final: 0.9175 (mpp) REVERT: m 150 MET cc_start: 0.9637 (tmm) cc_final: 0.9326 (ppp) REVERT: m 184 MET cc_start: 0.9025 (ppp) cc_final: 0.8395 (ppp) REVERT: m 188 ASP cc_start: 0.9831 (m-30) cc_final: 0.9625 (m-30) REVERT: n 4 MET cc_start: 0.9743 (ttt) cc_final: 0.9407 (tmm) REVERT: n 14 LEU cc_start: 0.9625 (mp) cc_final: 0.9287 (tp) REVERT: n 90 TYR cc_start: 0.9784 (m-80) cc_final: 0.9425 (m-80) REVERT: o 64 GLU cc_start: 0.9866 (tp30) cc_final: 0.9659 (tp30) REVERT: o 82 MET cc_start: 0.9450 (mtt) cc_final: 0.9215 (mmm) REVERT: o 93 TYR cc_start: 0.8816 (m-80) cc_final: 0.8542 (m-80) REVERT: o 127 MET cc_start: 0.8366 (mmt) cc_final: 0.7552 (mtt) REVERT: o 146 MET cc_start: 0.8769 (mtt) cc_final: 0.8546 (mtt) REVERT: p 14 MET cc_start: 0.9006 (ttt) cc_final: 0.8689 (tpp) REVERT: p 51 ILE cc_start: 0.9397 (tt) cc_final: 0.8994 (pt) REVERT: p 146 MET cc_start: 0.9720 (mpp) cc_final: 0.9339 (ptt) REVERT: p 149 MET cc_start: 0.8987 (mmp) cc_final: 0.8762 (mmm) REVERT: p 171 MET cc_start: 0.9743 (mmp) cc_final: 0.9331 (mmm) REVERT: q 1 MET cc_start: 0.5312 (ttt) cc_final: 0.4782 (tmm) REVERT: q 118 MET cc_start: 0.8420 (tpp) cc_final: 0.8067 (tpp) REVERT: q 167 LEU cc_start: 0.9861 (tt) cc_final: 0.9580 (mt) REVERT: r 82 LEU cc_start: 0.9926 (tt) cc_final: 0.9622 (tt) REVERT: r 100 MET cc_start: 0.9208 (mtt) cc_final: 0.8630 (tpp) REVERT: r 139 MET cc_start: 0.9580 (ttp) cc_final: 0.9086 (ptm) REVERT: t 5 MET cc_start: 0.9316 (mmp) cc_final: 0.9111 (mmm) REVERT: t 26 MET cc_start: 0.8743 (mmp) cc_final: 0.8075 (mmm) REVERT: t 42 ILE cc_start: 0.8809 (mt) cc_final: 0.8550 (mp) REVERT: t 43 MET cc_start: 0.9343 (tmm) cc_final: 0.9053 (tmm) REVERT: t 60 PHE cc_start: 0.9258 (t80) cc_final: 0.8371 (m-80) REVERT: t 62 TYR cc_start: 0.9797 (t80) cc_final: 0.9591 (t80) REVERT: t 96 MET cc_start: 0.9675 (mmm) cc_final: 0.8851 (tpt) outliers start: 3 outliers final: 2 residues processed: 727 average time/residue: 0.8949 time to fit residues: 1135.3619 Evaluate side-chains 621 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 619 time to evaluate : 8.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1201 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 710 optimal weight: 0.5980 chunk 910 optimal weight: 9.9990 chunk 705 optimal weight: 20.0000 chunk 1049 optimal weight: 0.0050 chunk 695 optimal weight: 6.9990 chunk 1241 optimal weight: 10.0000 chunk 776 optimal weight: 0.0570 chunk 756 optimal weight: 9.9990 chunk 573 optimal weight: 30.0000 overall best weight: 2.7316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 189 GLN U 421 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 235 GLN ** W 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN J 122 ASN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 220 ASN j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 188 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 103051 Z= 0.172 Angle : 0.668 14.670 139379 Z= 0.343 Chirality : 0.044 0.272 15874 Planarity : 0.005 0.112 18022 Dihedral : 6.542 89.532 14347 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.54 % Favored : 91.36 % Rotamer: Outliers : 0.02 % Allowed : 1.37 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.07), residues: 12934 helix: 0.27 (0.07), residues: 6041 sheet: -1.06 (0.12), residues: 1794 loop : -2.20 (0.09), residues: 5099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP W 80 HIS 0.011 0.001 HIS f 301 PHE 0.042 0.001 PHE U 728 TYR 0.026 0.001 TYR p 147 ARG 0.010 0.000 ARG d 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 734 time to evaluate : 8.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3527 (mtp) cc_final: 0.2544 (ptt) REVERT: b 7 MET cc_start: 0.5955 (tpp) cc_final: 0.5683 (tpp) REVERT: c 95 MET cc_start: 0.9794 (tpp) cc_final: 0.9354 (mmm) REVERT: c 97 ASP cc_start: 0.9650 (t70) cc_final: 0.9409 (p0) REVERT: c 167 MET cc_start: 0.8890 (mtp) cc_final: 0.8278 (tmm) REVERT: d 75 MET cc_start: 0.8675 (tpt) cc_final: 0.8268 (tpt) REVERT: d 116 HIS cc_start: 0.9095 (m90) cc_final: 0.8688 (m170) REVERT: e 67 MET cc_start: 0.3519 (mtt) cc_final: 0.3002 (mtt) REVERT: f 133 MET cc_start: 0.6260 (mtt) cc_final: 0.6054 (mtt) REVERT: f 209 MET cc_start: 0.7391 (ppp) cc_final: 0.5171 (mmt) REVERT: f 340 MET cc_start: 0.6169 (ptt) cc_final: 0.5512 (pmm) REVERT: f 469 TYR cc_start: 0.9011 (t80) cc_final: 0.8719 (t80) REVERT: f 670 MET cc_start: 0.8867 (mmp) cc_final: 0.8655 (mmm) REVERT: U 185 MET cc_start: 0.7526 (tmm) cc_final: 0.7234 (tpt) REVERT: U 325 MET cc_start: 0.8404 (ptm) cc_final: 0.8181 (mmp) REVERT: U 333 MET cc_start: 0.9461 (ppp) cc_final: 0.9178 (ppp) REVERT: U 423 MET cc_start: 0.9221 (mpp) cc_final: 0.8241 (ppp) REVERT: U 560 MET cc_start: 0.8931 (mmt) cc_final: 0.8390 (mmt) REVERT: U 675 MET cc_start: 0.9720 (mmm) cc_final: 0.9401 (tpp) REVERT: U 766 PHE cc_start: 0.9694 (t80) cc_final: 0.9470 (t80) REVERT: U 894 MET cc_start: 0.7995 (ttt) cc_final: 0.7571 (tmm) REVERT: V 37 MET cc_start: 0.9043 (mmm) cc_final: 0.8493 (mmm) REVERT: V 309 MET cc_start: 0.8931 (ptp) cc_final: 0.8626 (ptp) REVERT: V 409 MET cc_start: 0.9226 (ptp) cc_final: 0.8887 (ppp) REVERT: V 463 MET cc_start: 0.8604 (mmp) cc_final: 0.8371 (mmm) REVERT: W 16 MET cc_start: 0.8780 (mmt) cc_final: 0.7776 (mmt) REVERT: W 88 MET cc_start: 0.6287 (mtp) cc_final: 0.6001 (mtm) REVERT: W 451 MET cc_start: 0.8657 (mmp) cc_final: 0.8360 (mmp) REVERT: Y 73 MET cc_start: 0.8226 (mtp) cc_final: 0.7744 (ttm) REVERT: Y 104 MET cc_start: 0.9606 (tpp) cc_final: 0.9375 (tpp) REVERT: Y 152 MET cc_start: 0.5739 (mmp) cc_final: 0.4845 (mpp) REVERT: Y 282 MET cc_start: 0.7708 (mmt) cc_final: 0.7247 (mmt) REVERT: Y 302 HIS cc_start: 0.9201 (t70) cc_final: 0.8756 (t70) REVERT: Z 78 MET cc_start: 0.9040 (tpp) cc_final: 0.8522 (tpp) REVERT: Z 267 ARG cc_start: 0.9482 (mpt180) cc_final: 0.9191 (mmt180) REVERT: A 156 LYS cc_start: 0.9394 (tttt) cc_final: 0.9054 (tmtt) REVERT: A 256 MET cc_start: 0.9434 (mmp) cc_final: 0.9113 (mmm) REVERT: A 263 MET cc_start: 0.9418 (tpt) cc_final: 0.9080 (tpp) REVERT: A 299 MET cc_start: 0.8907 (ptp) cc_final: 0.8525 (ptp) REVERT: B 271 PHE cc_start: 0.9386 (m-80) cc_final: 0.9148 (m-80) REVERT: B 329 MET cc_start: 0.8239 (ppp) cc_final: 0.7851 (ppp) REVERT: B 405 MET cc_start: 0.9569 (mmm) cc_final: 0.8978 (mtp) REVERT: B 428 TYR cc_start: 0.9699 (m-80) cc_final: 0.9301 (m-80) REVERT: C 124 HIS cc_start: 0.8835 (t70) cc_final: 0.8389 (t70) REVERT: C 351 MET cc_start: 0.7667 (ttm) cc_final: 0.7320 (ttm) REVERT: D 296 MET cc_start: 0.8683 (tpt) cc_final: 0.8327 (tpt) REVERT: D 352 MET cc_start: 0.6085 (mpp) cc_final: 0.5708 (mpp) REVERT: E 102 MET cc_start: 0.9561 (pmm) cc_final: 0.9209 (mpp) REVERT: E 218 MET cc_start: 0.9463 (mmp) cc_final: 0.9189 (mmt) REVERT: E 352 MET cc_start: 0.9526 (tmm) cc_final: 0.9169 (tmm) REVERT: E 372 ARG cc_start: 0.9712 (mtt90) cc_final: 0.9296 (tmm160) REVERT: F 421 MET cc_start: 0.9651 (mmp) cc_final: 0.9401 (mmm) REVERT: G 19 GLU cc_start: 0.9630 (pm20) cc_final: 0.9414 (mp0) REVERT: G 83 MET cc_start: 0.9659 (mmp) cc_final: 0.9412 (mmm) REVERT: G 103 TYR cc_start: 0.9561 (t80) cc_final: 0.9144 (t80) REVERT: G 125 TYR cc_start: 0.9728 (m-80) cc_final: 0.9456 (m-80) REVERT: G 138 MET cc_start: 0.9390 (ttm) cc_final: 0.8937 (tpp) REVERT: H 156 PHE cc_start: 0.9149 (m-80) cc_final: 0.8942 (m-80) REVERT: I 45 LEU cc_start: 0.9920 (mt) cc_final: 0.9664 (tt) REVERT: J 38 ARG cc_start: 0.9541 (ttt180) cc_final: 0.9156 (mmp-170) REVERT: J 65 LEU cc_start: 0.9741 (mt) cc_final: 0.9533 (mt) REVERT: K 59 MET cc_start: 0.8817 (ttt) cc_final: 0.8402 (ttt) REVERT: K 143 PHE cc_start: 0.8845 (m-80) cc_final: 0.8236 (m-80) REVERT: K 156 MET cc_start: 0.8881 (tmm) cc_final: 0.8612 (tmm) REVERT: K 228 MET cc_start: 0.8205 (pmm) cc_final: 0.7721 (mpp) REVERT: L 108 LEU cc_start: 0.9777 (tt) cc_final: 0.9475 (mp) REVERT: L 153 TYR cc_start: 0.9044 (p90) cc_final: 0.8595 (p90) REVERT: L 176 MET cc_start: 0.9116 (ptp) cc_final: 0.8901 (ptp) REVERT: L 180 MET cc_start: 0.9245 (mmp) cc_final: 0.9011 (mmm) REVERT: M 27 MET cc_start: 0.9120 (mtt) cc_final: 0.8710 (mmm) REVERT: M 47 PHE cc_start: 0.8988 (m-10) cc_final: 0.8651 (m-10) REVERT: M 67 PHE cc_start: 0.7944 (m-10) cc_final: 0.7585 (m-10) REVERT: M 75 MET cc_start: 0.9345 (mtp) cc_final: 0.8957 (mmt) REVERT: M 135 PHE cc_start: 0.9580 (p90) cc_final: 0.9373 (p90) REVERT: M 184 MET cc_start: 0.8288 (ttp) cc_final: 0.8063 (ttm) REVERT: N 51 ASP cc_start: 0.9508 (m-30) cc_final: 0.9155 (t0) REVERT: N 84 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8940 (tttt) REVERT: N 119 MET cc_start: 0.9378 (mmt) cc_final: 0.8988 (mmp) REVERT: P 14 MET cc_start: 0.9519 (ttm) cc_final: 0.8761 (ttm) REVERT: P 96 TYR cc_start: 0.9710 (t80) cc_final: 0.9465 (t80) REVERT: P 117 PHE cc_start: 0.9235 (p90) cc_final: 0.8976 (p90) REVERT: P 146 MET cc_start: 0.9437 (mtm) cc_final: 0.9190 (ttm) REVERT: P 171 MET cc_start: 0.9627 (mmp) cc_final: 0.9394 (mmm) REVERT: Q 44 LEU cc_start: 0.9714 (tp) cc_final: 0.9360 (tp) REVERT: Q 69 MET cc_start: 0.9146 (mmm) cc_final: 0.8750 (mmm) REVERT: Q 118 MET cc_start: 0.8978 (tpt) cc_final: 0.8371 (tpp) REVERT: R 100 MET cc_start: 0.8303 (mtt) cc_final: 0.7884 (tpp) REVERT: S 74 MET cc_start: 0.9664 (ptp) cc_final: 0.9425 (ptp) REVERT: T 5 MET cc_start: 0.9131 (mmp) cc_final: 0.8903 (mmm) REVERT: T 26 MET cc_start: 0.8879 (mmp) cc_final: 0.7954 (mmm) REVERT: T 51 LEU cc_start: 0.9643 (tp) cc_final: 0.9410 (tp) REVERT: T 96 MET cc_start: 0.9587 (mmm) cc_final: 0.8501 (tpt) REVERT: T 127 MET cc_start: 0.7894 (ttp) cc_final: 0.6713 (ttm) REVERT: T 173 MET cc_start: 0.9717 (mmm) cc_final: 0.9284 (tpp) REVERT: T 214 MET cc_start: 0.9463 (mpp) cc_final: 0.9152 (mpp) REVERT: g 134 LEU cc_start: 0.9396 (mt) cc_final: 0.9043 (tp) REVERT: h 113 ARG cc_start: 0.9563 (mtt-85) cc_final: 0.9126 (mtm180) REVERT: i 25 MET cc_start: 0.9608 (mmp) cc_final: 0.9302 (mmm) REVERT: i 26 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9292 (mt-10) REVERT: i 110 LEU cc_start: 0.9792 (tt) cc_final: 0.9544 (mt) REVERT: i 174 MET cc_start: 0.9438 (ttm) cc_final: 0.9092 (mtp) REVERT: j 71 MET cc_start: 0.8355 (tmm) cc_final: 0.7684 (ppp) REVERT: j 106 TYR cc_start: 0.9648 (t80) cc_final: 0.9189 (t80) REVERT: j 133 ILE cc_start: 0.9424 (mp) cc_final: 0.9119 (tp) REVERT: k 48 LEU cc_start: 0.9705 (tp) cc_final: 0.9461 (tp) REVERT: k 78 MET cc_start: 0.8871 (ptp) cc_final: 0.8396 (ppp) REVERT: k 90 ASP cc_start: 0.9531 (t0) cc_final: 0.9242 (p0) REVERT: k 112 VAL cc_start: 0.9648 (t) cc_final: 0.9322 (t) REVERT: k 143 PHE cc_start: 0.9446 (m-10) cc_final: 0.9145 (m-10) REVERT: k 156 MET cc_start: 0.9466 (ppp) cc_final: 0.9240 (tmm) REVERT: l 86 ASN cc_start: 0.9817 (t0) cc_final: 0.9537 (m110) REVERT: l 115 LYS cc_start: 0.9597 (tptp) cc_final: 0.9242 (mmmm) REVERT: m 47 PHE cc_start: 0.9476 (m-10) cc_final: 0.8406 (m-10) REVERT: m 75 MET cc_start: 0.9504 (mpp) cc_final: 0.8839 (mpp) REVERT: m 135 PHE cc_start: 0.9392 (p90) cc_final: 0.8356 (p90) REVERT: m 150 MET cc_start: 0.9642 (tmm) cc_final: 0.9371 (ppp) REVERT: m 184 MET cc_start: 0.9307 (ppp) cc_final: 0.8802 (ppp) REVERT: n 4 MET cc_start: 0.9732 (ttt) cc_final: 0.9403 (tmm) REVERT: n 14 LEU cc_start: 0.9770 (mp) cc_final: 0.9317 (tp) REVERT: n 90 TYR cc_start: 0.9774 (m-80) cc_final: 0.9479 (m-80) REVERT: n 119 MET cc_start: 0.9624 (tpp) cc_final: 0.8718 (tpp) REVERT: o 82 MET cc_start: 0.9446 (mtt) cc_final: 0.9211 (mmm) REVERT: o 93 TYR cc_start: 0.8788 (m-80) cc_final: 0.8506 (m-80) REVERT: o 114 TYR cc_start: 0.8472 (m-80) cc_final: 0.8194 (m-80) REVERT: o 127 MET cc_start: 0.8366 (mmt) cc_final: 0.7470 (mtt) REVERT: o 146 MET cc_start: 0.8669 (mtt) cc_final: 0.8467 (mtt) REVERT: p 14 MET cc_start: 0.9032 (ttt) cc_final: 0.8735 (tpp) REVERT: p 51 ILE cc_start: 0.9399 (tt) cc_final: 0.9015 (pt) REVERT: p 149 MET cc_start: 0.8997 (mmp) cc_final: 0.8720 (mmp) REVERT: p 171 MET cc_start: 0.9704 (mmp) cc_final: 0.9291 (mmm) REVERT: q 1 MET cc_start: 0.5268 (ttt) cc_final: 0.4759 (tmm) REVERT: q 36 PHE cc_start: 0.8821 (m-10) cc_final: 0.8326 (m-80) REVERT: q 69 MET cc_start: 0.9549 (tpp) cc_final: 0.9183 (tpt) REVERT: q 118 MET cc_start: 0.8479 (tpp) cc_final: 0.8102 (tpp) REVERT: q 167 LEU cc_start: 0.9861 (tt) cc_final: 0.9593 (mt) REVERT: r 82 LEU cc_start: 0.9926 (tt) cc_final: 0.9634 (tt) REVERT: r 93 MET cc_start: 0.9325 (mtt) cc_final: 0.9026 (mtt) REVERT: r 100 MET cc_start: 0.9152 (mtt) cc_final: 0.7806 (mmm) REVERT: r 139 MET cc_start: 0.9575 (ttp) cc_final: 0.9082 (ptm) REVERT: t 5 MET cc_start: 0.9382 (mmp) cc_final: 0.9066 (mmm) REVERT: t 26 MET cc_start: 0.8687 (mmp) cc_final: 0.7971 (mmm) REVERT: t 42 ILE cc_start: 0.8744 (mt) cc_final: 0.8415 (mp) REVERT: t 43 MET cc_start: 0.9286 (tmm) cc_final: 0.8816 (tmm) REVERT: t 60 PHE cc_start: 0.9238 (t80) cc_final: 0.8195 (m-80) REVERT: t 70 MET cc_start: 0.9796 (mtm) cc_final: 0.9539 (ptp) REVERT: t 96 MET cc_start: 0.9654 (mmm) cc_final: 0.8827 (tpt) outliers start: 2 outliers final: 2 residues processed: 736 average time/residue: 0.8924 time to fit residues: 1144.5385 Evaluate side-chains 626 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 624 time to evaluate : 8.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 768 optimal weight: 40.0000 chunk 495 optimal weight: 10.0000 chunk 741 optimal weight: 0.8980 chunk 373 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 789 optimal weight: 5.9990 chunk 845 optimal weight: 8.9990 chunk 613 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 975 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 189 GLN U 421 GLN ** U 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 697 GLN ** U 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 880 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 GLN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 188 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 103051 Z= 0.210 Angle : 0.680 14.909 139379 Z= 0.352 Chirality : 0.044 0.277 15874 Planarity : 0.005 0.113 18022 Dihedral : 6.508 85.478 14347 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.05 % Favored : 90.85 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.07), residues: 12934 helix: 0.34 (0.07), residues: 6050 sheet: -1.06 (0.12), residues: 1797 loop : -2.16 (0.09), residues: 5087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP W 80 HIS 0.022 0.001 HIS f 301 PHE 0.035 0.002 PHE f 304 TYR 0.026 0.002 TYR S 75 ARG 0.019 0.001 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 693 time to evaluate : 9.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3565 (mtp) cc_final: 0.2562 (ptt) REVERT: b 7 MET cc_start: 0.5881 (tpp) cc_final: 0.5564 (tpp) REVERT: c 95 MET cc_start: 0.9821 (tpp) cc_final: 0.9375 (mmm) REVERT: c 97 ASP cc_start: 0.9643 (t70) cc_final: 0.9424 (p0) REVERT: c 167 MET cc_start: 0.8904 (mtp) cc_final: 0.8279 (tmm) REVERT: c 248 MET cc_start: 0.9556 (ppp) cc_final: 0.9292 (ppp) REVERT: d 95 MET cc_start: 0.3982 (mtt) cc_final: 0.3673 (mtp) REVERT: d 116 HIS cc_start: 0.9081 (m90) cc_final: 0.8679 (m170) REVERT: e 67 MET cc_start: 0.3668 (mtt) cc_final: 0.3188 (mtt) REVERT: f 133 MET cc_start: 0.6137 (mtt) cc_final: 0.5849 (mtt) REVERT: f 209 MET cc_start: 0.7422 (ppp) cc_final: 0.5203 (mmt) REVERT: f 469 TYR cc_start: 0.9061 (t80) cc_final: 0.8816 (t80) REVERT: f 670 MET cc_start: 0.8894 (mmp) cc_final: 0.8680 (mmm) REVERT: U 325 MET cc_start: 0.8420 (ptm) cc_final: 0.8153 (mmp) REVERT: U 333 MET cc_start: 0.9479 (ppp) cc_final: 0.9199 (ppp) REVERT: U 423 MET cc_start: 0.9250 (mpp) cc_final: 0.8318 (ppp) REVERT: U 560 MET cc_start: 0.9167 (mmt) cc_final: 0.8736 (mmt) REVERT: U 675 MET cc_start: 0.9739 (mmm) cc_final: 0.9417 (tpp) REVERT: U 766 PHE cc_start: 0.9731 (t80) cc_final: 0.9518 (t80) REVERT: U 894 MET cc_start: 0.8125 (ttt) cc_final: 0.7714 (tmm) REVERT: V 139 MET cc_start: 0.9058 (mpp) cc_final: 0.8853 (mpp) REVERT: V 409 MET cc_start: 0.9235 (ptp) cc_final: 0.8906 (ppp) REVERT: V 463 MET cc_start: 0.8506 (mmp) cc_final: 0.8289 (mmm) REVERT: W 16 MET cc_start: 0.8835 (mmt) cc_final: 0.7874 (mmt) REVERT: W 88 MET cc_start: 0.6223 (mtp) cc_final: 0.5922 (mtm) REVERT: W 312 MET cc_start: 0.6687 (ptt) cc_final: 0.6149 (ptt) REVERT: W 451 MET cc_start: 0.8610 (mmp) cc_final: 0.8372 (mmm) REVERT: X 306 LEU cc_start: 0.9317 (tt) cc_final: 0.8979 (mt) REVERT: Y 73 MET cc_start: 0.8307 (mtp) cc_final: 0.7721 (ttm) REVERT: Y 104 MET cc_start: 0.9611 (tpp) cc_final: 0.9366 (tpp) REVERT: Y 152 MET cc_start: 0.5781 (mmp) cc_final: 0.4900 (mpp) REVERT: Y 282 MET cc_start: 0.7791 (mmt) cc_final: 0.7306 (mmt) REVERT: Y 302 HIS cc_start: 0.9203 (t70) cc_final: 0.8752 (t70) REVERT: Z 78 MET cc_start: 0.8830 (tpp) cc_final: 0.8323 (tpp) REVERT: Z 267 ARG cc_start: 0.9479 (mpt180) cc_final: 0.9221 (mmt180) REVERT: A 156 LYS cc_start: 0.9352 (tttt) cc_final: 0.9067 (tmtt) REVERT: A 256 MET cc_start: 0.9429 (mmp) cc_final: 0.9051 (mmp) REVERT: A 263 MET cc_start: 0.9414 (tpt) cc_final: 0.9086 (tpp) REVERT: A 299 MET cc_start: 0.8949 (ptp) cc_final: 0.8567 (ptp) REVERT: A 430 MET cc_start: 0.7426 (tpt) cc_final: 0.7198 (tpt) REVERT: B 271 PHE cc_start: 0.9389 (m-80) cc_final: 0.9163 (m-80) REVERT: B 329 MET cc_start: 0.8303 (ppp) cc_final: 0.7885 (ppp) REVERT: B 405 MET cc_start: 0.9576 (mmm) cc_final: 0.8979 (mtp) REVERT: B 428 TYR cc_start: 0.9710 (m-80) cc_final: 0.9385 (m-80) REVERT: C 124 HIS cc_start: 0.8840 (t70) cc_final: 0.8395 (t70) REVERT: C 351 MET cc_start: 0.7678 (ttm) cc_final: 0.7325 (ttm) REVERT: D 214 MET cc_start: 0.9319 (ptp) cc_final: 0.8966 (ptp) REVERT: D 296 MET cc_start: 0.8737 (tpt) cc_final: 0.8387 (tpt) REVERT: D 352 MET cc_start: 0.5808 (mpp) cc_final: 0.5495 (mpp) REVERT: E 102 MET cc_start: 0.9536 (pmm) cc_final: 0.9284 (mpp) REVERT: E 218 MET cc_start: 0.9492 (mmp) cc_final: 0.9271 (mmm) REVERT: E 352 MET cc_start: 0.9538 (tmm) cc_final: 0.9196 (tmm) REVERT: E 372 ARG cc_start: 0.9726 (mtt90) cc_final: 0.9283 (tmm160) REVERT: F 421 MET cc_start: 0.9650 (mmp) cc_final: 0.9394 (mmm) REVERT: G 19 GLU cc_start: 0.9642 (pm20) cc_final: 0.9429 (mp0) REVERT: G 83 MET cc_start: 0.9671 (mmp) cc_final: 0.9397 (mmp) REVERT: G 125 TYR cc_start: 0.9725 (m-10) cc_final: 0.9451 (m-80) REVERT: G 138 MET cc_start: 0.9487 (ttm) cc_final: 0.9144 (tpp) REVERT: I 45 LEU cc_start: 0.9916 (mt) cc_final: 0.9636 (tt) REVERT: J 38 ARG cc_start: 0.9555 (ttt180) cc_final: 0.9122 (mmp-170) REVERT: J 71 MET cc_start: 0.8904 (tmm) cc_final: 0.8684 (tmm) REVERT: K 59 MET cc_start: 0.8884 (ttt) cc_final: 0.8452 (ttt) REVERT: K 78 MET cc_start: 0.9136 (pmm) cc_final: 0.8510 (pmm) REVERT: K 143 PHE cc_start: 0.8868 (m-80) cc_final: 0.8249 (m-80) REVERT: K 206 MET cc_start: 0.8080 (ptp) cc_final: 0.7780 (ptt) REVERT: K 228 MET cc_start: 0.8275 (pmm) cc_final: 0.7774 (mpp) REVERT: L 108 LEU cc_start: 0.9785 (tt) cc_final: 0.9482 (mp) REVERT: L 153 TYR cc_start: 0.9122 (p90) cc_final: 0.8661 (p90) REVERT: L 176 MET cc_start: 0.9137 (ptp) cc_final: 0.8934 (ptp) REVERT: L 180 MET cc_start: 0.9237 (mmp) cc_final: 0.9006 (mmm) REVERT: M 27 MET cc_start: 0.9167 (mtt) cc_final: 0.8727 (mmm) REVERT: M 47 PHE cc_start: 0.9009 (m-10) cc_final: 0.8632 (m-10) REVERT: M 67 PHE cc_start: 0.8085 (m-10) cc_final: 0.7712 (m-10) REVERT: M 75 MET cc_start: 0.9353 (mtp) cc_final: 0.8919 (mmt) REVERT: M 184 MET cc_start: 0.8338 (ttp) cc_final: 0.8119 (ttm) REVERT: N 51 ASP cc_start: 0.9512 (m-30) cc_final: 0.9178 (t0) REVERT: P 14 MET cc_start: 0.9480 (ttm) cc_final: 0.8617 (ttm) REVERT: P 117 PHE cc_start: 0.9243 (p90) cc_final: 0.9004 (p90) REVERT: P 146 MET cc_start: 0.9499 (mtm) cc_final: 0.9247 (ttm) REVERT: P 171 MET cc_start: 0.9560 (mmp) cc_final: 0.9323 (mmm) REVERT: P 204 MET cc_start: 0.8609 (mmp) cc_final: 0.8350 (mmp) REVERT: Q 44 LEU cc_start: 0.9730 (tp) cc_final: 0.9358 (tp) REVERT: Q 118 MET cc_start: 0.8940 (tpt) cc_final: 0.8213 (tpp) REVERT: S 74 MET cc_start: 0.9677 (ptp) cc_final: 0.9430 (ptp) REVERT: T 26 MET cc_start: 0.8892 (mmp) cc_final: 0.7903 (mmm) REVERT: T 51 LEU cc_start: 0.9656 (tp) cc_final: 0.9431 (tp) REVERT: T 96 MET cc_start: 0.9572 (mmm) cc_final: 0.8466 (tpt) REVERT: T 127 MET cc_start: 0.7918 (ttp) cc_final: 0.6729 (ttm) REVERT: T 173 MET cc_start: 0.9718 (mmm) cc_final: 0.9269 (tpp) REVERT: T 214 MET cc_start: 0.9454 (mpp) cc_final: 0.9151 (mpp) REVERT: g 134 LEU cc_start: 0.9411 (mt) cc_final: 0.9064 (tp) REVERT: i 25 MET cc_start: 0.9616 (mmp) cc_final: 0.9294 (mmm) REVERT: i 26 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9305 (mt-10) REVERT: i 174 MET cc_start: 0.9429 (ttm) cc_final: 0.9129 (mtp) REVERT: j 71 MET cc_start: 0.8152 (tmm) cc_final: 0.7558 (ppp) REVERT: j 106 TYR cc_start: 0.9636 (t80) cc_final: 0.9170 (t80) REVERT: j 133 ILE cc_start: 0.9481 (mp) cc_final: 0.9189 (tp) REVERT: k 78 MET cc_start: 0.8779 (ptp) cc_final: 0.8259 (ppp) REVERT: k 90 ASP cc_start: 0.9540 (t0) cc_final: 0.9250 (p0) REVERT: k 112 VAL cc_start: 0.9656 (t) cc_final: 0.9345 (t) REVERT: k 143 PHE cc_start: 0.9464 (m-10) cc_final: 0.9218 (m-10) REVERT: l 26 MET cc_start: 0.9466 (mmt) cc_final: 0.8876 (mmt) REVERT: l 86 ASN cc_start: 0.9829 (t0) cc_final: 0.9559 (m110) REVERT: l 115 LYS cc_start: 0.9624 (tptp) cc_final: 0.9261 (mmmm) REVERT: m 47 PHE cc_start: 0.9480 (m-10) cc_final: 0.8181 (m-10) REVERT: m 136 MET cc_start: 0.9498 (mtt) cc_final: 0.8462 (mtt) REVERT: m 150 MET cc_start: 0.9642 (tmm) cc_final: 0.9372 (ppp) REVERT: m 184 MET cc_start: 0.9357 (ppp) cc_final: 0.8833 (ppp) REVERT: n 4 MET cc_start: 0.9752 (ttt) cc_final: 0.9401 (ppp) REVERT: n 14 LEU cc_start: 0.9782 (mp) cc_final: 0.9364 (tp) REVERT: n 90 TYR cc_start: 0.9764 (m-80) cc_final: 0.9550 (m-80) REVERT: n 95 MET cc_start: 0.9677 (mpp) cc_final: 0.9390 (mpp) REVERT: n 119 MET cc_start: 0.9638 (tpp) cc_final: 0.8987 (tpp) REVERT: n 164 MET cc_start: 0.8644 (mtt) cc_final: 0.8412 (mmt) REVERT: o 82 MET cc_start: 0.9439 (mtt) cc_final: 0.9206 (mmm) REVERT: o 93 TYR cc_start: 0.8923 (m-80) cc_final: 0.8621 (m-80) REVERT: o 127 MET cc_start: 0.8458 (mmt) cc_final: 0.7847 (mtt) REVERT: o 146 MET cc_start: 0.8774 (mtt) cc_final: 0.8568 (mtt) REVERT: p 14 MET cc_start: 0.9036 (ttt) cc_final: 0.8695 (tpp) REVERT: p 149 MET cc_start: 0.9114 (mmp) cc_final: 0.8855 (mmp) REVERT: p 171 MET cc_start: 0.9694 (mmp) cc_final: 0.9335 (mmm) REVERT: q 69 MET cc_start: 0.9509 (tpp) cc_final: 0.9214 (tpt) REVERT: q 118 MET cc_start: 0.8537 (tpp) cc_final: 0.8171 (tpp) REVERT: q 167 LEU cc_start: 0.9869 (tt) cc_final: 0.9607 (mt) REVERT: r 82 LEU cc_start: 0.9924 (tt) cc_final: 0.9632 (tp) REVERT: r 97 MET cc_start: 0.9281 (mpp) cc_final: 0.8675 (tmm) REVERT: r 139 MET cc_start: 0.9583 (ttp) cc_final: 0.9112 (ptm) REVERT: t 26 MET cc_start: 0.8739 (mmp) cc_final: 0.8043 (mmm) REVERT: t 42 ILE cc_start: 0.8845 (mt) cc_final: 0.8585 (mp) REVERT: t 43 MET cc_start: 0.9284 (tmm) cc_final: 0.9044 (tmm) REVERT: t 60 PHE cc_start: 0.9273 (t80) cc_final: 0.8239 (m-80) REVERT: t 70 MET cc_start: 0.9806 (mtm) cc_final: 0.9555 (ptp) REVERT: t 96 MET cc_start: 0.9667 (mmm) cc_final: 0.8822 (tpt) REVERT: t 127 MET cc_start: 0.7481 (ttp) cc_final: 0.6619 (ttm) outliers start: 3 outliers final: 2 residues processed: 696 average time/residue: 0.8879 time to fit residues: 1080.1960 Evaluate side-chains 597 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 595 time to evaluate : 8.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1129 optimal weight: 2.9990 chunk 1189 optimal weight: 10.0000 chunk 1085 optimal weight: 2.9990 chunk 1156 optimal weight: 10.0000 chunk 1188 optimal weight: 5.9990 chunk 696 optimal weight: 10.0000 chunk 503 optimal weight: 3.9990 chunk 908 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 1045 optimal weight: 0.7980 chunk 1094 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 86 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 756 HIS ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 GLN V 319 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 79 ASN ** t 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 188 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 103051 Z= 0.167 Angle : 0.669 15.499 139379 Z= 0.341 Chirality : 0.044 0.354 15874 Planarity : 0.005 0.128 18022 Dihedral : 6.382 88.687 14347 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.43 % Rotamer: Outliers : 0.02 % Allowed : 0.73 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.07), residues: 12934 helix: 0.44 (0.07), residues: 6076 sheet: -0.97 (0.12), residues: 1815 loop : -2.11 (0.09), residues: 5043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP W 80 HIS 0.019 0.001 HIS f 301 PHE 0.032 0.001 PHE U 193 TYR 0.026 0.001 TYR K 26 ARG 0.013 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 711 time to evaluate : 9.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3461 (mtp) cc_final: 0.2488 (ptt) REVERT: b 7 MET cc_start: 0.5920 (tpp) cc_final: 0.5630 (tpp) REVERT: c 95 MET cc_start: 0.9832 (tpp) cc_final: 0.9386 (mmm) REVERT: c 97 ASP cc_start: 0.9624 (t70) cc_final: 0.9394 (p0) REVERT: c 189 ILE cc_start: 0.8852 (pt) cc_final: 0.8611 (tp) REVERT: c 226 MET cc_start: 0.7603 (tpt) cc_final: 0.7346 (tpt) REVERT: c 248 MET cc_start: 0.9562 (ppp) cc_final: 0.9352 (ppp) REVERT: d 116 HIS cc_start: 0.9090 (m90) cc_final: 0.8685 (m170) REVERT: e 67 MET cc_start: 0.3407 (mtt) cc_final: 0.2936 (mtt) REVERT: f 133 MET cc_start: 0.6071 (mtt) cc_final: 0.5818 (mtt) REVERT: f 209 MET cc_start: 0.7407 (ppp) cc_final: 0.5262 (mmt) REVERT: f 469 TYR cc_start: 0.9026 (t80) cc_final: 0.8694 (t80) REVERT: f 670 MET cc_start: 0.8896 (mmp) cc_final: 0.8681 (mmm) REVERT: U 188 MET cc_start: 0.5164 (ttt) cc_final: 0.4524 (ttt) REVERT: U 325 MET cc_start: 0.8376 (ptm) cc_final: 0.8175 (mmp) REVERT: U 333 MET cc_start: 0.9458 (ppp) cc_final: 0.8604 (pmm) REVERT: U 560 MET cc_start: 0.9205 (mmt) cc_final: 0.8778 (mmt) REVERT: U 675 MET cc_start: 0.9734 (mmm) cc_final: 0.9395 (tpp) REVERT: U 766 PHE cc_start: 0.9739 (t80) cc_final: 0.9526 (t80) REVERT: U 894 MET cc_start: 0.8020 (ttt) cc_final: 0.7612 (tmm) REVERT: V 409 MET cc_start: 0.9255 (ptp) cc_final: 0.8906 (ppp) REVERT: V 463 MET cc_start: 0.8499 (mmp) cc_final: 0.8280 (mmm) REVERT: V 494 MET cc_start: 0.9318 (ptp) cc_final: 0.8777 (ptt) REVERT: W 16 MET cc_start: 0.8797 (mmt) cc_final: 0.7836 (mmt) REVERT: W 88 MET cc_start: 0.6201 (mtp) cc_final: 0.5914 (mtm) REVERT: W 312 MET cc_start: 0.6661 (ptt) cc_final: 0.6437 (ptt) REVERT: W 326 MET cc_start: 0.8959 (ppp) cc_final: 0.8453 (ptt) REVERT: X 78 ASN cc_start: 0.9629 (t0) cc_final: 0.9307 (m-40) REVERT: Y 73 MET cc_start: 0.8227 (mtp) cc_final: 0.7729 (ttm) REVERT: Y 104 MET cc_start: 0.9611 (tpp) cc_final: 0.9381 (tpp) REVERT: Y 152 MET cc_start: 0.5784 (mmp) cc_final: 0.4984 (mpp) REVERT: Y 282 MET cc_start: 0.7630 (mmt) cc_final: 0.7155 (mmt) REVERT: Y 302 HIS cc_start: 0.9163 (t70) cc_final: 0.8712 (t70) REVERT: Z 78 MET cc_start: 0.9085 (tpp) cc_final: 0.8636 (tpp) REVERT: A 156 LYS cc_start: 0.9310 (tttt) cc_final: 0.9050 (tmtt) REVERT: A 256 MET cc_start: 0.9486 (mmp) cc_final: 0.9152 (mmp) REVERT: A 263 MET cc_start: 0.9414 (tpt) cc_final: 0.9087 (tpp) REVERT: A 299 MET cc_start: 0.8934 (ptp) cc_final: 0.8510 (ptp) REVERT: A 430 MET cc_start: 0.7384 (tpt) cc_final: 0.7155 (tpt) REVERT: B 214 MET cc_start: 0.8245 (ttt) cc_final: 0.7750 (ptm) REVERT: B 271 PHE cc_start: 0.9390 (m-80) cc_final: 0.9176 (m-80) REVERT: B 329 MET cc_start: 0.8320 (ppp) cc_final: 0.7897 (ppp) REVERT: B 405 MET cc_start: 0.9578 (mmm) cc_final: 0.9002 (mtp) REVERT: B 428 TYR cc_start: 0.9719 (m-80) cc_final: 0.9392 (m-80) REVERT: C 124 HIS cc_start: 0.8782 (t70) cc_final: 0.8343 (t70) REVERT: C 351 MET cc_start: 0.7771 (ttm) cc_final: 0.7437 (ttm) REVERT: D 296 MET cc_start: 0.8719 (tpt) cc_final: 0.8352 (tpt) REVERT: D 352 MET cc_start: 0.5865 (mpp) cc_final: 0.5543 (mpp) REVERT: E 102 MET cc_start: 0.9498 (pmm) cc_final: 0.9252 (mpp) REVERT: E 218 MET cc_start: 0.9482 (mmp) cc_final: 0.9259 (mmm) REVERT: E 352 MET cc_start: 0.9562 (tmm) cc_final: 0.9219 (tmm) REVERT: E 372 ARG cc_start: 0.9718 (mtt90) cc_final: 0.9316 (tmm160) REVERT: F 421 MET cc_start: 0.9649 (mmp) cc_final: 0.9373 (mmm) REVERT: G 83 MET cc_start: 0.9678 (mmp) cc_final: 0.9385 (mmp) REVERT: G 138 MET cc_start: 0.9410 (ttm) cc_final: 0.9004 (tpp) REVERT: H 156 PHE cc_start: 0.9149 (m-80) cc_final: 0.8927 (m-80) REVERT: I 45 LEU cc_start: 0.9929 (mt) cc_final: 0.9665 (tt) REVERT: J 38 ARG cc_start: 0.9562 (ttt180) cc_final: 0.9130 (mmp-170) REVERT: K 59 MET cc_start: 0.8908 (ttt) cc_final: 0.8546 (ttt) REVERT: K 78 MET cc_start: 0.9123 (pmm) cc_final: 0.8459 (pmm) REVERT: K 143 PHE cc_start: 0.8788 (m-80) cc_final: 0.8304 (m-80) REVERT: K 206 MET cc_start: 0.8029 (ptp) cc_final: 0.7762 (ptt) REVERT: K 228 MET cc_start: 0.8340 (pmm) cc_final: 0.7852 (mpp) REVERT: L 108 LEU cc_start: 0.9775 (tt) cc_final: 0.9453 (mp) REVERT: L 128 TYR cc_start: 0.8894 (m-10) cc_final: 0.8600 (m-10) REVERT: L 153 TYR cc_start: 0.9069 (p90) cc_final: 0.8588 (p90) REVERT: L 180 MET cc_start: 0.9245 (mmp) cc_final: 0.9030 (mmm) REVERT: M 27 MET cc_start: 0.9193 (mtt) cc_final: 0.8783 (mmm) REVERT: M 47 PHE cc_start: 0.8994 (m-10) cc_final: 0.8646 (m-10) REVERT: M 67 PHE cc_start: 0.8074 (m-10) cc_final: 0.7685 (m-10) REVERT: M 75 MET cc_start: 0.9333 (mtp) cc_final: 0.8856 (mmt) REVERT: M 135 PHE cc_start: 0.9578 (p90) cc_final: 0.9354 (p90) REVERT: M 184 MET cc_start: 0.8347 (ttp) cc_final: 0.8119 (ttm) REVERT: N 51 ASP cc_start: 0.9493 (m-30) cc_final: 0.9152 (t0) REVERT: N 84 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8612 (tttt) REVERT: N 86 MET cc_start: 0.9142 (tpt) cc_final: 0.8937 (tpt) REVERT: N 119 MET cc_start: 0.9403 (mmp) cc_final: 0.9063 (mmp) REVERT: P 14 MET cc_start: 0.9520 (ttm) cc_final: 0.8852 (ttm) REVERT: P 117 PHE cc_start: 0.9227 (p90) cc_final: 0.8977 (p90) REVERT: P 204 MET cc_start: 0.8458 (mmp) cc_final: 0.8167 (mmm) REVERT: Q 44 LEU cc_start: 0.9713 (tp) cc_final: 0.9364 (tp) REVERT: Q 69 MET cc_start: 0.9172 (mmm) cc_final: 0.8775 (mmm) REVERT: Q 118 MET cc_start: 0.9060 (tpt) cc_final: 0.8407 (tpp) REVERT: S 74 MET cc_start: 0.9681 (ptp) cc_final: 0.9391 (ptp) REVERT: T 5 MET cc_start: 0.9144 (mmp) cc_final: 0.8943 (mmm) REVERT: T 26 MET cc_start: 0.8735 (mmp) cc_final: 0.7782 (mmm) REVERT: T 96 MET cc_start: 0.9570 (mmm) cc_final: 0.8480 (tpt) REVERT: T 127 MET cc_start: 0.8102 (ttp) cc_final: 0.6972 (ttm) REVERT: T 173 MET cc_start: 0.9719 (mmm) cc_final: 0.9271 (tpp) REVERT: T 214 MET cc_start: 0.9463 (mpp) cc_final: 0.9136 (mpp) REVERT: g 134 LEU cc_start: 0.9416 (mt) cc_final: 0.9042 (tp) REVERT: i 25 MET cc_start: 0.9614 (mmp) cc_final: 0.9321 (mmp) REVERT: i 26 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9327 (mt-10) REVERT: i 90 LEU cc_start: 0.9770 (mt) cc_final: 0.9478 (mt) REVERT: i 174 MET cc_start: 0.9436 (ttm) cc_final: 0.9135 (mtp) REVERT: j 71 MET cc_start: 0.8209 (tmm) cc_final: 0.7628 (ppp) REVERT: j 106 TYR cc_start: 0.9626 (t80) cc_final: 0.9151 (t80) REVERT: j 133 ILE cc_start: 0.9459 (mp) cc_final: 0.9169 (tp) REVERT: k 48 LEU cc_start: 0.9716 (tp) cc_final: 0.9447 (tp) REVERT: k 78 MET cc_start: 0.8800 (ptp) cc_final: 0.8363 (ppp) REVERT: k 90 ASP cc_start: 0.9458 (t0) cc_final: 0.9201 (p0) REVERT: k 112 VAL cc_start: 0.9654 (t) cc_final: 0.9261 (t) REVERT: k 143 PHE cc_start: 0.9504 (m-10) cc_final: 0.9064 (m-10) REVERT: k 156 MET cc_start: 0.9338 (tmm) cc_final: 0.8876 (tmm) REVERT: l 26 MET cc_start: 0.9412 (mmt) cc_final: 0.8883 (mmt) REVERT: l 86 ASN cc_start: 0.9824 (t0) cc_final: 0.9571 (m110) REVERT: l 115 LYS cc_start: 0.9627 (tptp) cc_final: 0.9353 (mmmm) REVERT: m 47 PHE cc_start: 0.9439 (m-10) cc_final: 0.8421 (m-10) REVERT: m 75 MET cc_start: 0.9367 (mpp) cc_final: 0.8885 (mpp) REVERT: m 150 MET cc_start: 0.9625 (tmm) cc_final: 0.9371 (ppp) REVERT: m 184 MET cc_start: 0.9337 (ppp) cc_final: 0.8769 (ppp) REVERT: n 4 MET cc_start: 0.9737 (ttt) cc_final: 0.9386 (tmm) REVERT: n 14 LEU cc_start: 0.9759 (mp) cc_final: 0.9347 (tp) REVERT: n 119 MET cc_start: 0.9640 (tpp) cc_final: 0.9363 (mmm) REVERT: n 164 MET cc_start: 0.8724 (mtt) cc_final: 0.8490 (mmt) REVERT: o 54 MET cc_start: 0.9587 (mmt) cc_final: 0.9286 (mmm) REVERT: o 82 MET cc_start: 0.9439 (mtt) cc_final: 0.9208 (mmm) REVERT: o 93 TYR cc_start: 0.8920 (m-80) cc_final: 0.8614 (m-80) REVERT: o 114 TYR cc_start: 0.8616 (m-80) cc_final: 0.8380 (m-80) REVERT: o 127 MET cc_start: 0.8399 (mmt) cc_final: 0.7683 (mtt) REVERT: p 14 MET cc_start: 0.8970 (ttt) cc_final: 0.8675 (tpp) REVERT: p 51 ILE cc_start: 0.9449 (tt) cc_final: 0.9106 (pt) REVERT: p 149 MET cc_start: 0.9092 (mmp) cc_final: 0.8852 (mmp) REVERT: p 171 MET cc_start: 0.9704 (mmp) cc_final: 0.9344 (mmm) REVERT: q 36 PHE cc_start: 0.8824 (m-10) cc_final: 0.8332 (m-80) REVERT: q 69 MET cc_start: 0.9454 (tpp) cc_final: 0.9085 (tpt) REVERT: q 118 MET cc_start: 0.8449 (tpp) cc_final: 0.8068 (tpp) REVERT: q 167 LEU cc_start: 0.9848 (tt) cc_final: 0.9568 (mt) REVERT: r 82 LEU cc_start: 0.9908 (tt) cc_final: 0.9625 (tt) REVERT: r 100 MET cc_start: 0.9112 (mtt) cc_final: 0.7836 (mpp) REVERT: r 139 MET cc_start: 0.9584 (ttp) cc_final: 0.9122 (ptm) REVERT: t 5 MET cc_start: 0.9352 (mmp) cc_final: 0.9051 (mmm) REVERT: t 26 MET cc_start: 0.8656 (mmp) cc_final: 0.7648 (mmm) REVERT: t 42 ILE cc_start: 0.8727 (mt) cc_final: 0.8422 (mp) REVERT: t 43 MET cc_start: 0.9305 (tmm) cc_final: 0.8848 (tmm) REVERT: t 60 PHE cc_start: 0.9279 (t80) cc_final: 0.8234 (m-80) REVERT: t 70 MET cc_start: 0.9797 (mtm) cc_final: 0.9542 (ptp) REVERT: t 96 MET cc_start: 0.9672 (mmm) cc_final: 0.8791 (tpt) REVERT: t 127 MET cc_start: 0.7482 (ttp) cc_final: 0.6573 (ttp) outliers start: 2 outliers final: 2 residues processed: 713 average time/residue: 0.9021 time to fit residues: 1123.2792 Evaluate side-chains 620 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 618 time to evaluate : 8.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 1152 optimal weight: 10.0000 chunk 759 optimal weight: 0.9990 chunk 1223 optimal weight: 6.9990 chunk 746 optimal weight: 10.0000 chunk 580 optimal weight: 6.9990 chunk 850 optimal weight: 9.9990 chunk 1283 optimal weight: 6.9990 chunk 1181 optimal weight: 7.9990 chunk 1021 optimal weight: 8.9990 chunk 106 optimal weight: 0.0020 chunk 789 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 30 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 734 GLN ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 356 ASN ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 188 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 103051 Z= 0.200 Angle : 0.685 15.461 139379 Z= 0.352 Chirality : 0.044 0.317 15874 Planarity : 0.005 0.119 18022 Dihedral : 6.358 84.936 14347 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.07), residues: 12934 helix: 0.47 (0.07), residues: 6064 sheet: -0.98 (0.12), residues: 1813 loop : -2.10 (0.09), residues: 5057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP W 80 HIS 0.020 0.001 HIS f 301 PHE 0.032 0.002 PHE f 304 TYR 0.028 0.002 TYR S 75 ARG 0.011 0.001 ARG n 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25868 Ramachandran restraints generated. 12934 Oldfield, 0 Emsley, 12934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 691 time to evaluate : 9.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET d 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET e 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.3495 (mtp) cc_final: 0.2504 (ptt) REVERT: b 7 MET cc_start: 0.6020 (tpp) cc_final: 0.5701 (tpp) REVERT: c 95 MET cc_start: 0.9825 (tpp) cc_final: 0.9389 (mmm) REVERT: c 97 ASP cc_start: 0.9652 (t70) cc_final: 0.9431 (p0) REVERT: c 189 ILE cc_start: 0.8874 (pt) cc_final: 0.8654 (tp) REVERT: c 248 MET cc_start: 0.9570 (ppp) cc_final: 0.9344 (ppp) REVERT: d 116 HIS cc_start: 0.9073 (m90) cc_final: 0.8655 (m170) REVERT: e 67 MET cc_start: 0.4103 (mtt) cc_final: 0.3502 (mtt) REVERT: f 133 MET cc_start: 0.6063 (mtt) cc_final: 0.5794 (mtt) REVERT: f 209 MET cc_start: 0.7449 (ppp) cc_final: 0.5295 (mmt) REVERT: f 469 TYR cc_start: 0.9076 (t80) cc_final: 0.8786 (t80) REVERT: f 670 MET cc_start: 0.8923 (mmp) cc_final: 0.8571 (mmm) REVERT: U 188 MET cc_start: 0.5515 (ttt) cc_final: 0.4676 (ttt) REVERT: U 325 MET cc_start: 0.8464 (ptm) cc_final: 0.8177 (mmm) REVERT: U 333 MET cc_start: 0.9458 (ppp) cc_final: 0.8614 (pmm) REVERT: U 423 MET cc_start: 0.9323 (mpp) cc_final: 0.8365 (ppp) REVERT: U 560 MET cc_start: 0.9270 (mmt) cc_final: 0.8835 (mmt) REVERT: U 675 MET cc_start: 0.9747 (mmm) cc_final: 0.9409 (tpp) REVERT: U 766 PHE cc_start: 0.9741 (t80) cc_final: 0.9513 (t80) REVERT: U 894 MET cc_start: 0.8043 (ttt) cc_final: 0.7643 (tmm) REVERT: V 37 MET cc_start: 0.8957 (mmm) cc_final: 0.8692 (mmm) REVERT: V 139 MET cc_start: 0.9093 (mpp) cc_final: 0.8888 (mpp) REVERT: V 409 MET cc_start: 0.9266 (ptp) cc_final: 0.8939 (ppp) REVERT: V 494 MET cc_start: 0.9035 (ptp) cc_final: 0.8816 (ptt) REVERT: W 16 MET cc_start: 0.8770 (mmt) cc_final: 0.7681 (mmt) REVERT: W 88 MET cc_start: 0.6290 (mtp) cc_final: 0.5946 (mtm) REVERT: X 78 ASN cc_start: 0.9638 (t0) cc_final: 0.9309 (m-40) REVERT: Y 73 MET cc_start: 0.8306 (mtp) cc_final: 0.7705 (ttm) REVERT: Y 104 MET cc_start: 0.9597 (tpp) cc_final: 0.8901 (mmt) REVERT: Y 152 MET cc_start: 0.5653 (mmp) cc_final: 0.4955 (mpp) REVERT: Y 214 MET cc_start: 0.9312 (pmm) cc_final: 0.9101 (pmm) REVERT: Y 282 MET cc_start: 0.7645 (mmt) cc_final: 0.6994 (mmt) REVERT: Y 302 HIS cc_start: 0.9215 (t70) cc_final: 0.8774 (t70) REVERT: Z 78 MET cc_start: 0.8889 (tpp) cc_final: 0.8523 (tpp) REVERT: Z 267 ARG cc_start: 0.9499 (mpt180) cc_final: 0.9208 (mpt180) REVERT: A 138 MET cc_start: 0.9205 (ptp) cc_final: 0.8630 (mpp) REVERT: A 156 LYS cc_start: 0.9268 (tttt) cc_final: 0.9026 (tmtt) REVERT: A 256 MET cc_start: 0.9502 (mmp) cc_final: 0.9229 (mmm) REVERT: A 263 MET cc_start: 0.9419 (tpt) cc_final: 0.9094 (tpp) REVERT: A 299 MET cc_start: 0.8973 (ptp) cc_final: 0.8560 (ptp) REVERT: A 430 MET cc_start: 0.7386 (tpt) cc_final: 0.7125 (tpt) REVERT: B 214 MET cc_start: 0.8414 (ttt) cc_final: 0.7721 (ptm) REVERT: B 271 PHE cc_start: 0.9425 (m-80) cc_final: 0.9210 (m-80) REVERT: B 329 MET cc_start: 0.8401 (ppp) cc_final: 0.7954 (ppp) REVERT: B 405 MET cc_start: 0.9581 (mmm) cc_final: 0.9002 (mtp) REVERT: B 428 TYR cc_start: 0.9718 (m-80) cc_final: 0.9376 (m-80) REVERT: C 124 HIS cc_start: 0.8847 (t70) cc_final: 0.8405 (t70) REVERT: C 351 MET cc_start: 0.7778 (ttm) cc_final: 0.7440 (ttm) REVERT: D 214 MET cc_start: 0.9378 (ptp) cc_final: 0.9089 (ptp) REVERT: D 296 MET cc_start: 0.8745 (tpt) cc_final: 0.8390 (tpt) REVERT: D 352 MET cc_start: 0.5816 (mpp) cc_final: 0.5490 (mpp) REVERT: E 102 MET cc_start: 0.9541 (pmm) cc_final: 0.9269 (mpp) REVERT: E 218 MET cc_start: 0.9494 (mmp) cc_final: 0.9278 (mmm) REVERT: E 352 MET cc_start: 0.9579 (tmm) cc_final: 0.9245 (tmm) REVERT: E 372 ARG cc_start: 0.9726 (mtt90) cc_final: 0.9335 (tmm160) REVERT: F 175 MET cc_start: 0.9439 (ptp) cc_final: 0.9231 (mpp) REVERT: F 421 MET cc_start: 0.9646 (mmp) cc_final: 0.9363 (mmm) REVERT: G 83 MET cc_start: 0.9701 (mmp) cc_final: 0.9398 (mmp) REVERT: G 138 MET cc_start: 0.9468 (ttm) cc_final: 0.9181 (tpp) REVERT: H 156 PHE cc_start: 0.9156 (m-80) cc_final: 0.8930 (m-80) REVERT: I 45 LEU cc_start: 0.9923 (mt) cc_final: 0.9672 (tt) REVERT: J 38 ARG cc_start: 0.9572 (ttt180) cc_final: 0.9151 (mmp-170) REVERT: K 59 MET cc_start: 0.8982 (ttt) cc_final: 0.8646 (ttt) REVERT: K 143 PHE cc_start: 0.8906 (m-80) cc_final: 0.8334 (m-80) REVERT: K 156 MET cc_start: 0.8959 (tmm) cc_final: 0.8744 (tmm) REVERT: K 206 MET cc_start: 0.7996 (ptp) cc_final: 0.7647 (ptt) REVERT: K 228 MET cc_start: 0.8399 (pmm) cc_final: 0.7944 (mpp) REVERT: L 108 LEU cc_start: 0.9781 (tt) cc_final: 0.9461 (mp) REVERT: L 128 TYR cc_start: 0.8865 (m-10) cc_final: 0.8576 (m-10) REVERT: L 153 TYR cc_start: 0.9123 (p90) cc_final: 0.8627 (p90) REVERT: L 176 MET cc_start: 0.9080 (ptp) cc_final: 0.8866 (ptp) REVERT: L 180 MET cc_start: 0.9241 (mmp) cc_final: 0.9023 (mmm) REVERT: M 27 MET cc_start: 0.9222 (mtt) cc_final: 0.8807 (mmm) REVERT: M 47 PHE cc_start: 0.9027 (m-10) cc_final: 0.8631 (m-10) REVERT: M 67 PHE cc_start: 0.8098 (m-10) cc_final: 0.7700 (m-10) REVERT: M 75 MET cc_start: 0.9344 (mtp) cc_final: 0.8897 (mmt) REVERT: M 135 PHE cc_start: 0.9609 (p90) cc_final: 0.9404 (p90) REVERT: N 51 ASP cc_start: 0.9478 (m-30) cc_final: 0.9143 (t0) REVERT: N 84 LYS cc_start: 0.9198 (ttpp) cc_final: 0.8667 (ttmt) REVERT: N 86 MET cc_start: 0.9159 (tpt) cc_final: 0.8959 (tpt) REVERT: P 14 MET cc_start: 0.9484 (ttm) cc_final: 0.8844 (ttm) REVERT: P 117 PHE cc_start: 0.9247 (p90) cc_final: 0.9009 (p90) REVERT: P 204 MET cc_start: 0.8479 (mmp) cc_final: 0.8188 (mmm) REVERT: Q 44 LEU cc_start: 0.9730 (tp) cc_final: 0.9358 (tp) REVERT: Q 69 MET cc_start: 0.9227 (mmm) cc_final: 0.8849 (mmm) REVERT: Q 118 MET cc_start: 0.8977 (tpt) cc_final: 0.8288 (tpp) REVERT: S 74 MET cc_start: 0.9696 (ptp) cc_final: 0.9389 (ptp) REVERT: T 26 MET cc_start: 0.8780 (mmp) cc_final: 0.7808 (mmm) REVERT: T 96 MET cc_start: 0.9570 (mmm) cc_final: 0.8491 (tpt) REVERT: T 127 MET cc_start: 0.8048 (ttp) cc_final: 0.6864 (ttm) REVERT: T 173 MET cc_start: 0.9719 (mmm) cc_final: 0.9261 (tpp) REVERT: T 214 MET cc_start: 0.9455 (mpp) cc_final: 0.9139 (mpp) REVERT: g 134 LEU cc_start: 0.9433 (mt) cc_final: 0.9066 (tp) REVERT: i 25 MET cc_start: 0.9621 (mmp) cc_final: 0.9307 (mmp) REVERT: i 26 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9329 (mt-10) REVERT: i 110 LEU cc_start: 0.9805 (tt) cc_final: 0.9554 (mt) REVERT: i 174 MET cc_start: 0.9427 (ttm) cc_final: 0.9120 (mtp) REVERT: j 71 MET cc_start: 0.8231 (tmm) cc_final: 0.7646 (ppp) REVERT: j 106 TYR cc_start: 0.9647 (t80) cc_final: 0.9134 (t80) REVERT: j 133 ILE cc_start: 0.9440 (mp) cc_final: 0.9138 (tp) REVERT: k 48 LEU cc_start: 0.9721 (tp) cc_final: 0.9461 (tp) REVERT: k 78 MET cc_start: 0.8706 (ptp) cc_final: 0.8224 (ppp) REVERT: k 90 ASP cc_start: 0.9545 (t0) cc_final: 0.9227 (p0) REVERT: k 112 VAL cc_start: 0.9664 (t) cc_final: 0.9347 (t) REVERT: k 143 PHE cc_start: 0.9527 (m-10) cc_final: 0.9115 (m-10) REVERT: k 156 MET cc_start: 0.9262 (tmm) cc_final: 0.8833 (tmm) REVERT: l 26 MET cc_start: 0.9463 (mmt) cc_final: 0.8946 (mmt) REVERT: l 86 ASN cc_start: 0.9834 (t0) cc_final: 0.9594 (m110) REVERT: l 115 LYS cc_start: 0.9631 (tptp) cc_final: 0.9359 (mmmm) REVERT: m 47 PHE cc_start: 0.9365 (m-10) cc_final: 0.8390 (m-10) REVERT: m 75 MET cc_start: 0.9403 (mpp) cc_final: 0.8935 (mpp) REVERT: m 150 MET cc_start: 0.9624 (tmm) cc_final: 0.9366 (ppp) REVERT: m 184 MET cc_start: 0.9285 (ppp) cc_final: 0.8703 (ppp) REVERT: n 4 MET cc_start: 0.9742 (ttt) cc_final: 0.9350 (tmm) REVERT: n 14 LEU cc_start: 0.9735 (mp) cc_final: 0.9321 (tp) REVERT: n 119 MET cc_start: 0.9639 (tpp) cc_final: 0.8992 (tpp) REVERT: n 164 MET cc_start: 0.8763 (mtt) cc_final: 0.8494 (mmm) REVERT: o 54 MET cc_start: 0.9652 (mmt) cc_final: 0.9409 (mmm) REVERT: o 82 MET cc_start: 0.9427 (mtt) cc_final: 0.9199 (mmm) REVERT: o 93 TYR cc_start: 0.8953 (m-80) cc_final: 0.8627 (m-80) REVERT: o 114 TYR cc_start: 0.8657 (m-80) cc_final: 0.8419 (m-80) REVERT: o 127 MET cc_start: 0.8449 (mmt) cc_final: 0.7716 (mtt) REVERT: p 14 MET cc_start: 0.9043 (ttt) cc_final: 0.8694 (tpp) REVERT: p 149 MET cc_start: 0.9184 (mmp) cc_final: 0.8954 (mmp) REVERT: p 171 MET cc_start: 0.9720 (mmp) cc_final: 0.9411 (mmm) REVERT: q 69 MET cc_start: 0.9497 (tpp) cc_final: 0.9166 (tpt) REVERT: q 118 MET cc_start: 0.8513 (tpp) cc_final: 0.8143 (tpp) REVERT: q 167 LEU cc_start: 0.9856 (tt) cc_final: 0.9596 (mt) REVERT: r 82 LEU cc_start: 0.9909 (tt) cc_final: 0.9624 (tt) REVERT: r 93 MET cc_start: 0.9434 (mtm) cc_final: 0.9056 (ptp) REVERT: r 100 MET cc_start: 0.9005 (mtt) cc_final: 0.7798 (mpp) REVERT: r 139 MET cc_start: 0.9539 (ttp) cc_final: 0.9046 (ptm) REVERT: t 5 MET cc_start: 0.9298 (mmp) cc_final: 0.9004 (mmm) REVERT: t 26 MET cc_start: 0.8635 (mmp) cc_final: 0.7680 (mmm) REVERT: t 42 ILE cc_start: 0.8822 (mt) cc_final: 0.8621 (mp) REVERT: t 43 MET cc_start: 0.9336 (tmm) cc_final: 0.9064 (tmm) REVERT: t 60 PHE cc_start: 0.9300 (t80) cc_final: 0.8285 (m-80) REVERT: t 70 MET cc_start: 0.9812 (mtm) cc_final: 0.9563 (ptp) REVERT: t 96 MET cc_start: 0.9666 (mmm) cc_final: 0.8796 (tpt) REVERT: t 127 MET cc_start: 0.7509 (ttp) cc_final: 0.6677 (ttm) outliers start: 3 outliers final: 2 residues processed: 694 average time/residue: 0.9021 time to fit residues: 1098.8989 Evaluate side-chains 605 residues out of total 11148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 603 time to evaluate : 8.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1288 random chunks: chunk 626 optimal weight: 0.9980 chunk 811 optimal weight: 9.9990 chunk 1088 optimal weight: 0.0040 chunk 313 optimal weight: 7.9990 chunk 942 optimal weight: 40.0000 chunk 150 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 1023 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 1050 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 416 GLN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN Z 77 ASN ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN D 65 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 218 GLN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.035188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.024022 restraints weight = 1361022.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.025000 restraints weight = 875237.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.025720 restraints weight = 625661.980| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 103051 Z= 0.190 Angle : 0.678 15.385 139379 Z= 0.348 Chirality : 0.044 0.282 15874 Planarity : 0.005 0.121 18022 Dihedral : 6.328 83.078 14347 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.16 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.08), residues: 12934 helix: 0.53 (0.07), residues: 6069 sheet: -0.96 (0.12), residues: 1841 loop : -2.07 (0.09), residues: 5024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP W 80 HIS 0.019 0.001 HIS f 301 PHE 0.032 0.002 PHE f 304 TYR 0.021 0.001 TYR N 138 ARG 0.011 0.001 ARG Y 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21247.38 seconds wall clock time: 377 minutes 47.97 seconds (22667.97 seconds total)